My theory on the alternate drive might be right (assuming you can't boot from a software RAID) there is info in the console log that mentions a prior boot parittion that no longer exists. Any ideas on how to clear this up?
1/1/13 12:29:25.280 PM com.apple.kextd[12]: Warning: /Volumes/DATA/System/Library/Extensions: No such file or directory
1/1/13 12:29:25.281 PM com.apple.kextd[12]: /Volumes/DATA/System/Library/PrivateFrameworks/EFILogin.framework/Resources/EFI ResourceBuilder.bundle/Contents/Resources: No such file or directory
1/1/13 12:29:26.278 PM com.apple.kextd[12]: Warning: /Volumes/DATA/System/Library/Extensions: No such file or directory
1/1/13 12:29:26.279 PM com.apple.kextd[12]: /Volumes/DATA/System/Library/PrivateFrameworks/EFILogin.framework/Resources/EFI ResourceBuilder.bundle/Contents/Resources: No such file or directory
1/1/13 12:29:26.284 PM com.apple.kextd[12]: '/Volumes/DATA' updating, delaying reboot.
1/1/13 12:29:26.364 PM com.apple.kextcache[6743]: Warning: /Volumes/DATA/System/Library/Extensions: No such file or directory
1/1/13 12:29:26.367 PM com.apple.kextcache[6743]: /Volumes/DATA/System/Library/PrivateFrameworks/EFILogin.framework/Resources/EFI ResourceBuilder.bundle/Contents/Resources: No such file or directory
1/1/13 12:29:26.760 PM com.apple.kextcache[6744]: /Volumes/DATA locked; waiting for lock.
1/1/13 12:29:27.709 PM com.apple.kextcache[6743]: Error copying /Volumes/DATA/System/Library/Caches/com.apple.kext.caches/Startup/kernelcache to /Volumes/Boot OS X/com.apple.boot.S/System/Library/Caches/com.apple.kext.caches/Startup/kernelca che
1/1/13 12:29:28.526 PM com.apple.kextcache[6743]: Error copying /Volumes/DATA/System/Library/Caches/com.apple.kext.caches/Startup/kernelcache to /Volumes/Boot OS X/com.apple.boot.S/System/Library/Caches/com.apple.kext.caches/Startup/kernelca che
1/1/13 12:29:28.633 PM com.apple.kextd[12]: kextcache error while updating /Volumes/DATA (error count: 2)
1/1/13 12:29:28.634 PM com.apple.kextd[12]: /Volumes/DATA is still busy, delaying reboot.
1/1/13 12:29:28.634 PM com.apple.kextcache[6744]: Warning: /Volumes/DATA/System/Library/Extensions: No such file or directory
1/1/13 12:29:28.634 PM com.apple.kextcache[6744]: /Volumes/DATA/System/Library/PrivateFrameworks/EFILogin.framework/Resources/EFI ResourceBuilder.bundle/Contents/Resources: No such file or directory
1/1/13 12:29:29.184 PM com.apple.kextcache[6744]: Error copying /Volumes/DATA/System/Library/Caches/com.apple.kext.caches/Startup/kernelcache to /Volumes/Boot OS X/com.apple.boot.S/System/Library/Caches/com.apple.kext.caches/Startup/kernelca che
1/1/13 12:29:29.880 PM com.apple.kextcache[6744]: Error copying /Volumes/DATA/System/Library/Caches/com.apple.kext.caches/Startup/kernelcache to /Volumes/Boot OS X/com.apple.boot.S/System/Library/Caches/com.apple.kext.caches/Startup/kernelca che
1/1/13 12:29:29.957 PM com.apple.kextd[12]: kextcache error while updating /Volumes/DATA (error count: 3)
1/1/13 12:29:29.957 PM com.apple.kextd[12]: Warning: /Volumes/DATA/System/Library/Extensions: No such file or directory
1/1/13 12:29:29.958 PM com.apple.kextd[12]: /Volumes/DATA/System/Library/PrivateFrameworks/EFILogin.framework/Resources/EFI ResourceBuilder.bundle/Contents/Resources: No such file or directory