With the problems still happening after all this time and the number of users affected it is looking very much like the Window 7/2008 compatible drivers won’t work with Windows Server 2003 print servers. Print queues on a 2003 print server are having serious problems but queues on a 2008 server are unaffected. Next step is to switch all the print queues to a 2008 server with any Brother queues using Winprint instead of BrPrint.
At the moment I am also trying 2008 R2’s feature of isolating the difficult Brother driver as well. I’m holding my breath to see if it works.
Unfortunately since applying some of these changes to my own accounts I am seeing an increasing trend of my computers taking a very long time to complete the application of GPP printer settings in particular, the dreaded extremely long GPO processing that is a “feature” of Windows 7 and Vista. This demands an article of its own to try to analyse what is happening (we don’t see this to the same extent, if at all, in XP). I have thought that it may be due to needing the policy settings to allow unattended printer installation but the computers concerned are in the correct group so a lot more work is needed to try to nail down what is happening. There seems to be a similar effect on other elements of system startup (e.g. System Event Notification Service) so perhaps it is just coincidental.