After cloning my internal drive to an external drive using Carbon Copy Cloner and booting from the external drive once (then booting from my internal drive again), Time Machine thinks that every single file on my computer has changed. How can I fix this?
Details: I recently installed Carbon Copy Cloner and made a clone of my drive to an external. The external is partitioned into two parts - one for the clone, and one for Time Machine. The Time Machine partition predates the clone partition. Last night I ran a first clone and backed up everything, so I left my computer open. Time Machine ran a couple backups overnight and everything was fine. This morning I booted from the external disk to make sure the clone was working. Once I booted from my internal drive again and opened up Time Machine to run a backup, it took a very long time to calculate then finally decided to attempt to back up my entire hard drive again. I've tried ejecting the clone volume (even though it is excluded from backup) and of course a restart, to no avail.
I am running a late-2011 15" MacBook Pro with Mavericks.