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Open an existing J2SE project and copy files to the clipboard. Create a new J2SE project and paste the files into its sources node. What what happens to the Edit toolbar icons - they flash repeatedly - it appears that each file is pasted atomically and briefly changes the selected node. The selected node should only be affected at the end of the paste operation - this is just doing lots of extra work for no reason.
The reason why the editor icons blink is very likely in the fact that after a copy is done, the java source is post processed in memory (becomes modified) which enables Save All action. Then the source is saved and another processed which results in blinking. There is hardly anything core could do with this. This is all in hands of java module. Possible fix is to disable this behaviour (maybe already done due to refactoring changes) or modify all the copied files and save all of them at once.
I'm sorry, I don't see any blinking. Please reopen this issue if you can reproduce it in promo-D. It is possible, that this issue is Mac OS X specific (Tim?) but OS of this issue is All and I cannot reproduce it on my Windows machine -> WORKSFORME