With all due respect to boRg, I doubt a change to any permission functionality is going to change your situation. I've done several searches of your messages and found that even in cases where the result is zero records, the timeout still results. That means that the sub-query of the main query doesn't have time to complete within the timeout.
I ran this query on your site: SELECT tblTopic.Topic_ID, tblTopic.Forum_ID, tblTopic.Poll_ID, tblTopic.No_of_views, tblTopic.Subject FROM tblTopic WHERE tblTopic.Topic_ID IN (SELECT tblThread.Topic_ID FROM tblThread WHERE ( tblThread.Message LIKE '%jetta golf gti abdbflashada%')) ORDER BY tblTopic.Last_entry_date DESC;
The result could not possibly return a result yet the timeout would expire 4 out of 5 times, so the sub-query "(SELECT tblThread.Topic_ID FROM tblThread WHERE ( tblThread.Message LIKE '%jetta golf gti abdbflashada%'))" is probably where the problem starts. The problem with the subquery is that it's doing a query against the message field which is a 'text' datatype. This problem exists for the entire SQL world (Oracle, MS SQL, MySQL, MS Access, etc). To get acceptable performance when doing text/memo/long searches you need to use something like the Full-Text Search or simply speed up the machine running SQL Server.
Is your SQL Server running on a dedicated machine? What kind of hardware is it running on? Does it have plenty of memory?
However, given the fact that I did get a response in 1 of the 5 attempts of the same search, extending the timeout even further might work.
I wish I could get your data to do a test run on my MySQL-based WWF. I think all forum developers eventually start using the Full-text indexing option and then start using Natural Language searches when the forum data gets large.