Could it be something going on with Adobe Audition??

The reason I mention that is because for recording my guitar parts I always use Adobe Audition V1.5, a program I've had forever but continue to use because I've never found anything better, including newer versions of Audition, for recording/editing audio. So in audition I have the BIAB WAV file and then record my guitar parts to separate WAV files.

I then import the audio WAV files of my guitar parts into reaper where I do the final mixing with all the individual BIAB files. Sometimes, but not always, the WAV file I created with audition is not in sync with the other files in the reaper project and I need to shift it around.