I have resolved my problem.
Along with our library we have this controller that has an LCD display and it shows what the library is doing, Loading, Unloading, Rewinding, BOT, how much is left on your tape, etc. That unit has always been there for years, in fact I thought it was necessary for the library, but the library also had two SCSI ports.
As a last ditch effort, I bypassed that controller connected the SCSI cable directly from the server to the library and "TA-DA" it worked. I dont think our extra controller is bad because it used to work fine when we had v4.5FP6, I just think it's some sort of incompatability with version 6.
This would explain why when I sent the library in to have the firmware updated they didnt find any problems. They probably didnt use a controller board like ours.
So now things are working fine and we have another useless piece of equipment.