It's a known bug. Version 11 is supposed to have fixed it and I've never experienced it in Version 11 myself. Here's a possible solution from the SCS users website. (Well, not a solution but you can detect the problem before you take the time to encode your output).
Subject: RE: More on Changed media? SSD??
Reply by: Gary James
Date: 7/3/2012 4:25:56 PM
I've just placed version v1.0.34 of Timeline Tools on the web site. This include some bug fixes and a new display filter that shows only those events that have a mismatch between the Take name displayed in the event, and the media file name that was the source of the take.
This is especially useful for those of you who've experienced the infamous Sony Vegas Changed Media bug.
Steve Mann
MannMade Digital Video
http://www.mmdv.com