After many calls to Citrix and with Microsoft and with no help or suggestions from either(at least non that made sense). We finally fixed it by creating different farms.
Yes it is harder to manage but now we can reboot a server and use with in 10 minutes again instead of an 1 1\2 hours. We didn’t even know we could do this till we read about it in the XenApp 6 documentation. We are currently using XenApp 4.5, so we thought we would take a look. It actually isn’t do difficult to set up. Just add the new farm to the web interface and move a server to the new farm. All you need is a SQL server in the same location as the servers.
Right now there really aren’t any down falls. I am sure we will run in to some. It did take a while to move all the servers and to reset permissions. But this also allowed us to clean it up a little bit.
We have 8 servers in that farm. Normally it would take us 3 or 4 days to update all the software but we were able to do this in a day and half. It only took that long because we had to wait for user’s to drain off the servers.
Now if we can just get everything moved over to XenApp 6…