So here's one we've been working, no solution as of yet...

PC prior to SP3 is SP2 with all current patches, BM is 3.9sp2 and the server is 6.5sp8 with all current patches. Client is 4.91sp5. CLNTRUST is loaded from the edir login script. with a DWNTRUST proceeding it. CLNTRUST is the version that comes with BM3.9SP2. Windows Firewall is disabled by GPO.

We push out SP3 and after reboot, the user gets the prompt to login to BM. reboot the pc 1, 2, 3, 4, up to 8 times to get it to work normally, it does work eventually.,

What's causing it to fail? it's not on every machines, but some do take up to 8 reboots to use CLNTRUST again