There is no reason to assume there is a problem with Parallels 9.
It's possible that you have an hardware problem that causes data corruption, either with the disk or the RAM.
Run disk utility.app to diagnose the disk, do a 'verify disk' on all your internal disks/partitions.
Run Apple Diagnostics: http://support.apple.com/en-us/HT202731
You should also run CHKDSK on Windows.
Although Time Capsule is very convenient over a wireless connection it's considerably slow for moving so much data, consider connecting directly via a wired connection.
Last edited: Jan 20, 2015