Eclipse Flash programmer quirks

I have several SW projects defined in Eclipse. I have noticed that sometimes the flash programmer utility will indicate "problem with target board", and the <Program> button will be greyed out. The <Run> option will always work though. After trying several things including re-compiles, full rebuilds, shutting down and re-opening Eclipse, I eventually get the flash programmer to work - I just don&#39;t know what fixed it.

All this time I have been starting Eclipse from the start menu. The last time I had the problem I shut Eclipse down and started Quartus and SOPC builder and started Eclipse from there. The programmer worked. Is this just a coincidence or have others noticed this behavior?

thanks