Well, this answer is a bazillion years late based on the original date of the problem, but ...
I found that if the test agent (QTAgent32.exe) crashes or dies before completing the full sequence, then AssemblyInitialize (and possibly ClassInitialize and TestInitialize) will be called. For example, put this in your [AssemblyCleanup] function and you will see what happens:
Process p = AutotestShared.RunProcess("cmd", "/c taskkill /t /f /im QTAgent32.exe", true); p.WaitForExit();
So, the moral of this story: check your cleaning features to see if there are crashes / corruption. Failures during cleanup are not displayed in the test report because the skip / fail statements are already completed. But the problems that it causes can manifest themselves in other ways.
user910866
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