Buggy Transient Markers. Need Help!!

I've never seen this behaviour with transient markers.  Sounds like something's become corrupted either in the Sonar install or possibly even your video driver.  I'd suggest trying uninstalling and reinstalling both. 
 
As I understand it, this behaviour should never occur under any circumstances, so there are no settings changes which can fix it. 
 
Have transient markers worked fine for you previously?
 
Have you installed any software from when transient markers were working (presuming they were) and when they started behaving oddly?  That's another possible culprit.
 
It might be worth giving your computer a sweep for malicious software too perhaps.
 
Case in point, I had a recent issue where a project I was working on was always causing Sonar to crash when loading the project.  It had loaded fine earlier that evening.  The auto-save backups also crashed Sonar.  The backups on a separate hard drive from a week previous were also crashing Sonar.  I had not installed any new plugins or software between when the project loaded and when it didn't, which meant that a piece of software somewhere had become corrupted.  Uninstalling and reinstalling Sonar did not fix the problem.  I then created a blank project and systematically loaded every soft synth and effect that my project was using until I found the problem.  It was a very recent effect, CamelSpace, whose DLL had become corrupted.  Uninstall/reinstall fixed the problem.  On that very same evening, my audio card driver software had also gone completely bananas, displaying really weird menu items.  Again, an uninstall/reinstall cycle fixed it.  The thing is, file systems / hard drives can and do glitch out from time to time and the only way to rectify the problem is to replace the files with uncorrupted ones by reinstalling.
 
That's my best guess anyway :-)