I thought it may help someone else if they are in the same situation.
I spent a great deal of time working on getting our lighting system ironed out. We have a clean install of Windows 7 64-bit, running ShowXpress 6.25 with BOX driver 1.04 and sometimes we can run fine for a few hours then randomly the X-Factor will go into standalone mode and the Control Board application locks and I have to kill the exe. I then downloaded the latest fix_for_windows.zip and replaced the Controlboard.exe file and the issue still exists, but it is hard to track down as I can't reproduce the issue at will.
After redoing all circuts, yes we also have an opto isolator...still happening. I tried to put together anything common that was happeneing each time and the only thing I could point to that was common was the movement of the mouse, no seriously. The mouse is the only other USB device on the system and I thought it may be worth trying a USB PCI card to get the xfactor off of the same USB bus. Sure enough that fixed it! We have been rock solid for > 1 month now and I am very glad I can put this problem to rest.