Well, I've fixed one of the problems. Zipcloud support told me that their application does not work very well with App Nap, so I had to permanently disable that specifically for the Zipcloud app.
I still have the following problems:
1) External HD's have been reformatted and time machine seems to work, but it can take a long while for the HD's to mount properly and for Time Machine to start (sometimes hours)
2) MBP still freeezing - no idea why, I don't have a lot of system extensions or junk software. I use Native Instruments Traktor Scratch Pro and there don't appear to be any issues reported with the latest version and Mavericks on the NI forums.
3) Disk Utility is still reporting every time I run it that the disk needs to be repaired in Recovery HD mode but when I do this DU still subsequently reports the same thing
I reinstalled Mavericks and ran the Apple Hardware Test but no joy...here's the results of my Etrecheck scan if anyone would be kind enough to cast their eye over them:
Hardware Information:
MacBook Pro (Retina, 15-inch, Early 2013)
MacBook Pro - model: MacBookPro10,1
1 2.8 GHz Intel Core i7 CPU: 4 cores
16 GB RAM
Video Information:
Intel HD Graphics 4000 - VRAM: 1024 MB
NVIDIA GeForce GT 650M - VRAM: 1024 MB
Audio Plug-ins:
BluetoothAudioPlugIn: Version: 1.0
AirPlay: Version: 1.9
AppleAVBAudio: Version: 2.0.0
iSightAudio: Version: 7.7.3
System Software:
OS X 10.9 (13A603) - Uptime: 0 days 0:7:7
Disk Information:
APPLE SSD SM768E disk0 : (751.28 GB)
EFI (disk0s1) <not mounted>: 209.7 MB
disk0s2 (disk0s2) <not mounted>: 750.42 GB
Recovery HD (disk0s3) <not mounted>: 650 MB
USB Information:
Apple Inc. MacBook Air SuperDrive
Apple Inc. FaceTime HD Camera (Built-in)
Apple Inc. Apple Internal Keyboard / Trackpad
Apple Inc. BRCM20702 Hub
Apple Inc. Bluetooth USB Host Controller
FireWire Information:
Thunderbolt Information:
Apple Inc. thunderbolt_bus
Kernel Extensions:
com.Cycling74.driver.Soundflower (1.5.3)
Problem System Launch Daemons:
Problem System Launch Agents:
Launch Daemons:
[loaded] com.adobe.fpsaud.plist
[loaded] com.adobe.SwitchBoard.plist
[loaded] com.google.keystone.daemon.plist
[loaded] com.microsoft.office.licensing.helper.plist
[loaded] com.orbicule.uc.plist
[failed] com.rogueamoeba.hermes.plist
Launch Agents:
[not loaded] com.adobe.AAM.Updater-1.0.plist
[loaded] com.adobe.CS5ServiceManager.plist
[loaded] com.google.keystone.agent.plist
[loaded] com.orbicule.UCAgent.plist
User Launch Agents:
[loaded] com.adobe.AAM.Updater-1.0.plist
[loaded] com.adobe.ARM.[...].plist
User Login Items:
GrowlHelperApp
iTunesHelper
EvernoteHelper
Dropbox
CrossOver CD Helper
ZipCloud
NIHardwareAgent
3rd Party Preference Panes:
Flash Player
Flip4Mac WMV
Native Instruments USB Audio
Internet Plug-ins:
AdobePDFViewer.plugin
AdobePDFViewerNPAPI.plugin
AmazonMP3DownloaderPlugin1016264.plugin
AmazonMP3DownloaderPlugin101749.plugin
Default Browser.plugin
Flash Player.plugin
FlashPlayer-10.6.plugin
Flip4Mac WMV Plugin.plugin
googletalkbrowserplugin.plugin
iPhotoPhotocast.plugin
JavaAppletPlugin.plugin
npgtpo3dautoplugin.plugin
o1dbrowserplugin.plugin
OfficeLiveBrowserPlugin.plugin
QuickTime Plugin.plugin
SharePointBrowserPlugin.plugin
Silverlight.plugin
User Internet Plug-ins:
WebEx64.plugin
Bad Fonts:
None
Time Machine:
Skip System Files: NO
Auto backup: YES
Volumes being backed up:
Destinations:
GC HD [Local] (Last used)
Total size: 999.86 GB
Total number of backups: 15
Oldest backup: 2013-10-28 00:22:19 +0000
Last backup: 2013-11-04 06:44:15 +0000
Size of backup disk: Excellent
Backup size 999.86 GB > (Disk size Zero KB X 3)
Top Processes by CPU:
40% ZipCloud
3% WindowServer
1% fontd
1% EtreCheck
0% com.apple.WebKit.Networking
0% ps
0% Dropbox
0% loginwindow
0% uc
0% Safari
Top Processes by Memory:
197 MB Safari
115 MB ZipCloud
98 MB WindowServer
98 MB Dock
98 MB com.apple.IconServicesAgent
82 MB Dropbox
82 MB mds_stores
66 MB com.apple.WebKit.WebContent
49 MB com.apple.WebKit.Networking
49 MB SystemUIServer
Virtual Memory Statistics:
10.27 GB Free RAM
3.75 GB Active RAM
550 MB Inactive RAM
1.43 GB Wired RAM
292 MB Page-ins
0 B Page-outs