I see a Command Timeout of 1600 seconds from fresh installs on both my test VM and production/physical box right in the SMC under Settings->Notification Server->Database Settings. With the imposed ASP script timeout of 90 seconds in IIS and a 1600 CMDB command timeout, I'm guessing any SQL queries will bomb should they exceed 90 secs.
FYI: In comparison, my Altiris 6.x server has a command timeout of 600 secs which in my opinion is also an excessive value. However, won't matter if IIS ASP script timeout will ultimately determine how long a query runs.
Clint