Hey Matt,
My suggestion is to do the easiest stuff first.
1. Re-install Cubase.
2. If your recordings are still out of time, try using system restore and pick a restore date just before the trouble started. If it clears up, you can be more careful as to what you install afterwards that may affect your audio stream. It makes good sense to create a restore point just before installing anything major. Saves lots of time should something get corrupted ?
3. You didn't mention what sound card you're using, but as long as it is an ASIO capable device, try downloading ASIO 4 ALL
http://www.asio4all.com/
It is a great, free, very low latency driver that works with ASIO capable sound cards. I get far less latency using it instead of the vendor's drivers for my sound card!! This is not likely your problem, but you should see performance gains nonetheless.
4. Check back here regularly, as it is likely that someone has had similar trouble and may reply to this thread.
