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Ubuntu never hides any folders, just for your information. I use Ubuntu as a primary operating system and I know this. It only disallows you to open them if they are restricted, but it never hides them.

Seems to me they got corrupted. Maybe a virus attack? NTFS is easily recognised by Ubuntu.

The best thing to do is to completely re-install windows 7 but backup everything from your Ubuntu OS. Everything that you can. 

SOMETIMES, however, its possible that a particular partition is not mounted. This can happen. However it should still show your Hard Disk divisions in Disk Utility Under Administraion Under System.

i.e. System -> Administration -> Disk Utility -> (Select your Hard Drive)