I've been having the same problem, which just started in the past few days. At the same time, my Mac Pro started swapping position of my two screens whenever I rebooted after it wouldn't wake up. Perhaps coincidentally the same time there was an update to El Cap - that I hadn't yet loaded. Any suggestions would be appreciated.
Ari
7/20/16 6:32:10.208 PM powerd[49]: com.apple.message.domain: com.apple.darkwake.capable
com.apple.message.hardware_support: smc_without_platform
com.apple.message.settings: ac
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/20/16 9:19:12.531 PM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Normal Sleep
com.apple.message.signature2: Idle Sleep
com.apple.message.signature3: HID Activity
com.apple.message.signature4: HID Activity
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/20/16 10:52:09.692 PM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Normal Sleep
com.apple.message.signature2: Idle Sleep
com.apple.message.signature3: Maintenance
com.apple.message.signature4: Maintenance
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/20/16 11:53:00.518 PM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Normal Sleep
com.apple.message.signature2: Maintenance Sleep
com.apple.message.signature3: Maintenance
com.apple.message.signature4: Maintenance
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 1:27:12.005 AM powerd[49]: com.apple.message.domain: com.apple.darkwake.capable
com.apple.message.hardware_support: smc_without_platform
com.apple.message.settings: ac
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 1:27:14.897 AM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Normal Sleep
com.apple.message.signature2: Maintenance Sleep
com.apple.message.signature3: Maintenance
com.apple.message.signature4: Maintenance
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 4:40:55.880 AM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Normal Sleep
com.apple.message.signature2: Maintenance Sleep
com.apple.message.signature3: SleepTimer
com.apple.message.signature4: SleepTimer
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 6:21:59.908 AM powerd[49]: com.apple.message.domain: com.apple.sleepwake.failure
com.apple.message.signature3: Sleep
com.apple.message.signature: Interest Failure
com.apple.message.value: 5
com.apple.message.summarize: NO
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 6:21:59.908 AM powerd[49]: com.apple.message.domain: com.apple.sleep.failure
com.apple.message.signature: Interest Failure
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 6:21:59.908 AM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Unknown
com.apple.message.signature3: Unknown
com.apple.message.signature4: Unknown
com.apple.message.result: fail
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 8:32:44.511 AM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Normal Sleep
com.apple.message.signature2: Software Sleep
com.apple.message.signature3: HID Activity
com.apple.message.signature4: HID Activity
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 10:04:04.260 AM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Normal Sleep
com.apple.message.signature2: Idle Sleep
com.apple.message.signature3: Maintenance
com.apple.message.signature4: Maintenance
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 11:10:09.909 AM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Normal Sleep
com.apple.message.signature2: Maintenance Sleep
com.apple.message.signature3: Maintenance
com.apple.message.signature4: Maintenance
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 12:05:27.924 PM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Normal Sleep
com.apple.message.signature2: Maintenance Sleep
com.apple.message.signature3: SleepTimer
com.apple.message.signature4: SleepTimer
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 3:26:27.194 PM powerd[49]: com.apple.message.domain: com.apple.darkwake.capable
com.apple.message.hardware_support: smc_without_platform
com.apple.message.settings: ac
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 3:26:35.247 PM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Standby
com.apple.message.signature2: Maintenance Sleep
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 4:27:33.772 PM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Standby
com.apple.message.signature2: Maintenance Sleep
com.apple.message.signature3: Maintenance
com.apple.message.signature4: Maintenance
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/21/16 5:28:31.553 PM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Standby
com.apple.message.signature2: Maintenance Sleep
com.apple.message.signature3: Maintenance
com.apple.message.signature4: Maintenance
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/22/16 8:27:16.008 AM powerd[49]: com.apple.message.domain: com.apple.darkwake.capable
com.apple.message.hardware_support: smc_without_platform
com.apple.message.settings: ac
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/22/16 8:27:23.056 AM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Standby
com.apple.message.signature2: Maintenance Sleep
com.apple.message.signature3: SleepTimer
com.apple.message.signature4: SleepTimer
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/22/16 9:51:52.516 AM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Normal Sleep
com.apple.message.signature2: Idle Sleep
com.apple.message.signature3: HID Activity
com.apple.message.signature4: HID Activity
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/22/16 11:02:44.599 AM powerd[49]: com.apple.message.domain: com.apple.sleepwake.failure
com.apple.message.signature3: Sleep
com.apple.message.signature: Interest Failure
com.apple.message.value: 9
com.apple.message.summarize: NO
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/22/16 11:02:44.600 AM powerd[49]: com.apple.message.domain: com.apple.sleep.failure
com.apple.message.signature: Interest Failure
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/22/16 11:02:44.600 AM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Unknown
com.apple.message.signature3: Unknown
com.apple.message.signature4: Unknown
com.apple.message.result: fail
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673
7/22/16 12:16:18.514 PM powerd[49]: com.apple.message.domain: com.apple.sleepwake.type
com.apple.message.signature: Normal Sleep
com.apple.message.signature2: Idle Sleep
com.apple.message.signature3: HID Activity
com.apple.message.signature4: HID Activity
com.apple.message.result: pass
com.apple.message.summarize: YES
SenderMachUUID: 92ADD38D-8CC8-3E09-A4CF-D6E451305673