Looking for advice,

I have a server running multiple VMs.  Freenas, and two instances of Windows 7.  Hardware includes two Xeon 5520's, 36GB of ram, 2 6450 (one in 8x slot and one in 16x slot), and two Intel M1505 sata cards.  Each Win7 VM has USB ports and a ATI 6450 with passthrough.  I use these VMs as KODI/XBMC frontends.  Both machines are working and the passthrough and drivers seems to be properly installed.  However, I am having a very frustrating issue.  Overtime, the video output and/or audio output gets choppy or ceases to work.  Restarting the VM does not resolve the issue, but if I reboot the entire server, the 6450 work again.  This is very frustrating because rebooting the server properly with the three VMs takes at least 30 minutes.  I have reserved the memory for all three VMs, but I have not done the PCI hole end/start config.  Would this resolve this issue?  If not what could be the problem?  After alot of research, most people it either works or it doesn't.  I have not been able to find any suggestions about my issue. 

Thanks