I have few flexunit test cases . When I am running those testcases from Flashbuilder FlexUnit plugin I am able to run all the testcases and when I run Build file to run those testcases , build file is launching my testrunner swf file and it is throwing follwoing runtime error in flash player
VerifyError: Error #1014: Class flash.events::NativeWindowBoundsEvent could not be found.
We had a similar problem in my project. Took a lot of research and trial and error, but we finally narrowed it down to the resource.properties file. Turns out that if the file gets too big it causes this problem. Extending the timeout doesn't help. You have to break your resource.properties into more granular files to reduce the file size. This seems to fix the problem. We have had it happen several times since then and we know how to fix it, so we get it fixed pretty quickly.
Not sure if this will fix your problem, but it fixed ours.
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