You have Boot Camp with Windows and Parallels with another version of Windows and OS X. Parallels is a good product but it leaks over and affects OS X in unexpected ways. I have and do experience this myself.
You have a worse case of it, there are ways to mitigate it however.
First is repairing permissions, this PDF explains that.
Then a pram reset when things get strange,
To do a PRAM reset, you need to restart your machine and hold down these 4 keys all together at the same time.
‘Option’, ‘Command (Cloverleaf or Apple)’, ‘R’ and 'P' all together at the same time.
Keep them down until you hear 4 startup chimes, this is the sound that your computer makes when it starts up, it is like a boonngg. The screen should also cycle from white to black and then back to white along with the chimes.
The sound should also get louder.
If you have a wireless keyboard then the procedure is a little bit different.
Use the very same keys but wait until the first chime and immediately press and hold those keys. I recommend getting your fingers ready because timing is critical.
It can take many tries to get it, any USB keyboard is preferable.
If using a Windows keyboard then substitute the Control key for the Command key and Alt for Option, all others stay the same.
This resets all of the system buses on your computer, USB, FireWire, display, ethernet and your keyboard/mouse/trackpad.
This will correct many faults but not necessarily yours.
Those will help a lot.