I'm grasping here...

Use SQL Trace to capture the command that are being sent to SQL Server. Start a trace and then fire up your app. If it doesn't start in "slow" mode, start over again. Repeat until the app starts in "slow" mode <g>. Check the trace for anything that doesn't look right.

Does your server have enough memory? Are you running any other applications on the same server? Maybe Exchange?

-Mike