I have a webpage that takes 10 minutes to run one query against a database, but the same query returns in less than a second when run from SQL Server Management Studio.
Is there any difference between the command text of the query in the app and the query you are executing manually? Since you said that reindexing helps performance (which also updates statistics), it sounds like it may be getting stuck on a bad execution plan.
You might want to run a sql trace and capture the showplanxml event to see what the execution plan looks like, and also capture sql statement complete (though this can slow the server down if a lot of statements are coming through the system so be careful) to be sure the statement sent to SQL server is the same one you are running manually.