Ok Sebastian, it looks like when you changed the start up settings and then rebooted, you corrupted the sync between any associated files or folders through Windows Live Sync.
The problems caused when connecting any external hdd stem from the same issue, which is why a disk check helped, if only a little.
So, how to fix the problem? It's a bit hard to help with this without taking a look at your pc, but here are some suggestions.
-go through every folder or external hdd that you've synced in the past.
-if possible, remove any that you don't need or use anymore and re-sync any that you do.
-if your successful check for an up to date version of Windows Live Sync. I think it's now called Windows Live Mesh.
-possibly check and make note of what you have set up on W.L.S and remove any if you feel it's necessary before you change any settings or remove files or folders.
If none of the above solves your problem, let me know.