Just had this problem occur as well.
All the workspaces seem to now have the Flash Player Icons on the menu. They were not there before.
If I create a new workspace, it seems to work fine until I switch to any existing workspace and then the new workspace is also affected.
I can import a project from the other workspaces, into a new workspace and that works as well.
My only mental history is that all was well. Then I spent some time writing a project in CS4 for a day without any need for Flex Builder. Then when I returned to FLex Builder the last opened project would not run and although I can get to the new project screen, the next and Finish button although enabled fail silently.
Eclipse Galieo, Flash 4 Builder Plugin.
Not sure what path to take. Remove Flex Builder plugin? Exclipse? Certain files or hidden folders?
Any suggestions where to explore would be nice.
Not sure the cause but I resorted to cleaning Eclipse each time it starts, and for the time being this seems to help.
Since this box was Windows I just added "-clean" to the shortcut properties.
The author of the post implies to keep this for a bit and then remove once it appears the environment seems stable.
It's four years later and this was the solution to my problem with CF Builder 3. When trying to edit an HTML page I was getting the error:
Plug-in "com.adobe.editor.html" was unable to instantiate class "com.adobe.editor.html.core.HTMLEditor".
Adding "-clean" to the end of the start command fixed the problem. See the link above.