I THINK I FOUND THE SOLUTION!!!
What got me on track of the problem was colrim's post about Maverick being the problem. I have access to a few Macs at my work and one of them doesn't have Maverick installed yet but it does have InDesign CC on it, although not in use. So I fired up InDesign CC on that Mac and no saving problem! So could Maverick be the problem indeed? No! I noticed that copy of CC didn't have our companies default settings installed yet so I closed ID CC, copied the proper preferences into the Library, started ID CC again and... the saving problem was there again!
This led me to the conclusion there has to be something in the preferences that's causing this constant prompt to save even unchanged documents!
The next step was quite logical: I deleted the pref file and restart ID CC with new default settings. No more saving problem again: good! I then simply changed every setting screen by screen, so I first changed all General settings to our companies preference and opened a test document: no saving problem. I changed all Sync Settings, no problem, all Interface settings, no problem, etc. etc. and then I got to the Guide & Pasteboard settings: after changing those settings I immediately got the saving problem again!
So I reset all setting on that screen to default and now changed them one by one to see if a specific setting caused the problem and the first one was the right one: so here is what I believe is the cause and thus also the solution to this nagging problem:
go to Preferences > Guides & Pasteboard > DISABLE Preview background - Match to Theme Color.
That should be it! As soon as you enable it, you will get that nagging save problem again! I would love to see you all give this a try to confirm my findings. If this is indeed the problem then 1. you have the solution and 2. maybe Adobe can fix this because it seems a bit like a little bug to me. I can happily live with this setting off though.