Windows and OS X keep track of time differently. Windows uses local time while OS X uses UTC.
Unfortunately, the problem you are experiencing is perfectly normal.
You have one of two options: 1) Turn off time syncing for one OS. The time for this OS will always be incorrect, but the time for the other will always be correct, or 2) turn on time syncing for both OSs. Both will start out incorrect when you first boot the computer, but eventually it will correct itself.
Personally, I would go for option #1. One OS will always have the wrong time, but as long as you know it's wrong, you won't have any problems.