Sonar X1 Producer Expanded: RANDOMLY No Audio In or Out

Been using the program for a few months. Worked without a hitch.

All of a sudden I have this problem:

When i hit record the program works for about 5 seconds, then everything stops. X1 doesn't exactly freeze though, what happens is the sound turns off, the clip stops at the moment where the sound vanished (no continuing red recording line on the track), and the program's buttons react to mouse clicks but with a lot of lag. From that No-Sound moment onward there is no sign that sound is coming into or out of the program. When I press play the bar (again with a lot of lag) starts moving as it normally does when listening to playback, except no sound comes out of the speakers, and the tracks' input sound meters stay frozen where they were the minute the sound disappeared. Master sound meter as well. Basically it appears the flow of sound is severed.

Comp Details: Asus desktop that runs on Windows 7 (x64), and has 16 GBs of Ram

Recent Events That May Be the Cause of this Problem (?)
(unfortunately all these things happened roughly around the same time, adding to my confusion...)

- I Opened up a project file that was made using Music Creator 5
     - the problem didn't happen until i started trying to record something new into this file using Sonar
- I Installed the Sonar X1d patch
     - the problem was noticed after I installed the X1d patch
- A Trojan virus was found on my computer
      - the problem was noticed about the same time I found out about the Trojan
      - I have since rebooted my computer and reinstalled Sonar X1 (as well as the X1d patch)
                      - The program lasted a few seconds longer than usual before repeating the problem, much to my stressed dismay.

Extra Info:

- Sonar doesn't give any message that it's a "dropout" when this happens.
- I've already checked the "share drivers with other programs" box
- Before I rebooted the computer I ran 2 virus scans that reported there was no sign of a virus
- When the problem first happened the program used to record for a few seconds at least whenever I'd close and re-open it. And it would even play the project in its entirety (with FX and all) without any problems. It's when i would try to record that that stoppage would occur and sometimes the lag would even begin when I would press the "input echo" button before starting to record. However after my last attempt it's opening up with the post-problem lag already present without any actions from me. Because all those things happened in the same period of time, and because this problem is continuing after I've rebooted the entire computer, what I'm left assuming is that the trojan virus corrupted that particular project file and that my computer has now just gotten re-corrupted since I reopened that exact project to try again. Any help would be greatly appreciated as I have to finish that particular project by the end of this month. Thank you.

When a virus scanner finds a trojan, it often moves the file into a safe area, tries to repair it, or completely removes that file. If that file is crucial for the functionality of a program or hardware (like a library or driver file), you are in trouble. I hope you have either a log file from the virus scanner, or made notations what is removed/put into the vault/repaired. This might give you a clue what is going wrong and how to repair it.