Mac – Can MacBooks backup when in hibernation mode

There could be any number of different factors involved in why Time Machine is doing a full scan after using Windows/Bootcamp. From what you describe it seems out of sync, as if your system is telling Time Machine 'this volume is not like it was, so do a full scan'. One of the first things that might give you an idea of what is going on would be to open Console immediately after Time Machine kicks in with 'Preparing...'. By observing fseventsd, system.log, and backupd you should be able to get a better picture of what might be taking place. You can type any of those terms in the search box of Console to see a consolidated list of those events.

This article is also an excellent in-depth guide to Time Machine; it covers just about everything you could imagine, so take a look.

So here's what happened:

I took the computer to the AppleStore, seeing it was only about three weeks old, and got them to take a look at it. Since it's a company computer I had some company benefits granting me a temporary replacement while they were fixing mine. I took my TimeMachine copy and restored it on to the borrowed Mac. I was surprised to find that the issue still appeared, which was quite annoying. So I restored the Mac again, messed around with the pmsetsettings and tried to reproduce the issue but it was impossible.

I then remembered that the issue started appearing a few days ago when I did a battery calibration (Drained the Mac completely) so I restored to a TimeMachine backup from before that and Boom, the issue was gone. At about the same time they called from the store and said that they couldn't reproduce the issue, so I told them what I had found, came in and got my computer back.

All in all, a really weird story but apparently something related to draining the battery while the computer was still on got corrupted and was then included in the TimeMachine backup.