I believe I solved our problem.
First, during the SP 6 install I chose Windows Authentication. I know for a fact all previous updates were installed using SQL Authentication.
So, I shut down BESAlert.exe (to stop the emails), Started the BES Server Configuration utility and switched back to SQL Authentication - but the password failed. Shut down all the BB services. Open SQL Enterprise Manager (we use MSDE for BES, but I have SQL servers throughout the network, so I have access to the SQL Ent. Mgr) and change the SQL user password for the user for BES. Go back into the BES Server Configuration utility and set the SQL login info. Test connection, and it passed.
Reboot everything for good measure. Everything works, except I'm still getting those errors in the Application Event Log.
<N/A> | BlackBerry Controller (Application Event Log on BESSERVER) | 07/22/2008 13:33:17 (EFFF2710) -> [DIAG] Error telling the debug trace file position : Invalid argument (error : 22)
I look at the log files for the day, and the CTRL log is over 5 gigs! Just a hunch, but I think that is going to be a problem.
Shut down all the BB services again. Rename the folder for the daily log files. Reboot the server so that a new folder is created.
Everything is working fine now.....
I still need to move the BES server off the MSDE to a proper SQL server, but not today....