Sorry to hear this. What version of Visual Assist are you using? Have you installed update 1 for VS2013? I vaguely remember similar problems but those problems were fixed in a recent build of Visual Assist. I tried but wasn't able to reproduce the problem using VA2031 and VS2013 update 1.
If you still see the problems using the latest Visual Assist build: Are your project files placed on a network drive? Can you please turn on logging, reproduce the problem and collect the logs? http://support.wholetomato.com/default.asp?W305