Recently, I was trying to upgrade to FusionReactor 4.0.8 because I was getting alot of "too many files open" error on my Mac (Lion), which that release addresses. I'm not sure why, but for some reason I kept getting an error during upgrade that:

FusionReactor Administration Manager is Still Running
Please manually stop the fram process daemon and press Continue once you have ensured the server is shut down.

I pinged the FusionReactor email list and quickly got an answer (from their CTO Darren Pywell no less) that 1) my situation was rare and, 2) if this happens, you can resolve it by shutting down FRAM as follows:

cd /Applications/FusionReactor/tomcat/bin
./framd stop

To start the service again, you use:
./framd start

I continue to be impressed with FusionReactor as a product, as well as their prompt and accurate support!