SQL Execution (Enterprise Manager-QA) VS. .NET Execution

I have been chasing an issue for quite a while where the query would timeout when executed from an ASP.NET interface. If I ran that exact same query through Query Analyzer the results would be returned in less than 2 seconds. I have for a while been struggling with why it is different between those two interfaces. I thought about connection pooling issues, command time outs and connection timeouts and was focused on that for a while.