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Well, the summary can't describe it as much as I would. It simply happens whenever I shutdown/start up my own Tomcat instance and the another one - the one that was already defined is highlighed transparently. It didn't happen with IDE built from the sources two days ago so it's a bug that was introduced during those 2 past days. It might be that it shows up in the module, but can also be more IDE generic. See the screenshot for more details. It should clear things up entirely :)
Created attachment 22315 [details] Transparent highlighting of inactive tomcat instance
Works for me on WinXP SP2, JDK 1.5.0_03 in build 200505252000. If you can still reproduce, please try it again with clean userdir and provide more OS/JDK info and then reopen this issue. Thanks.