configuration variable 'compiler.verbose-stacktraces' must only be set once
I think your facing this problem for standalone FLEX application & for projects in workspace, Flex compiler is getting compiling information from
..\Program Files\Adobe\Flex Builder 3 Plug-in\sdks\2.0.1\frameworks\flex-config.xml for such projects.
& for Web projects it refers project\WEB-INF\flex\flex-config.xml
You can try to modify setting in this file. Hope this will work for you.