Flashing Java permission window happening after update 15. What to do?

I am runnning OS X 10.6.8 on a

Model Identifier: MacPro5,1

Processor Name: Quad-Core Intel Xeon

Processor Speed: 2.4 GHz

with my Firewall up and I installed the suggested Java update 15 a few days ago and now I am getting the flashing window that is too fast to respond to popping up. I didn't have this happeing before the update so I am assuming it was the update that is causing the problem. I've looked for a answer but I can't see to find one on how to get rid of the flashing window (it's driving me a little crazy). If I turn the firewall off it stops, but I don't want to keep the firewall down. I am also running little snitch, but it's not telling me that anything is happening when the java window pops up and goes away. Anyone having this problem or a answer? Thanks.