I have not seen this behavior. Rather than mess with it now I would try the project in an earlier version of AE. When you get some time carefully document your workflow, OS and system details and file a bug report.
Since I do not know your workflow in detai it's hard for me to recommend an alternative. I seldom hold down the Ctrl/Cmnd and scrub audio because there are much more efficient ways to find audio sync. You might consider adding labeled markers in Audition. They show up when the sound file is imported int AE and they show up in the timeline.