Samkry,
I am not aware of any SQL Server related configuration that will time out a query. Some middle tier applications and web servers will do so, but I am not familiar with any default configuration that will stop a query from running.
As far as capturing the recompiled stored procedures, Profiler would be the right tool to capture the metrics. Once you load Profiler, click on the Events Selection Tab, then click on the 'Show all Events' check box on the bottom right, scroll down to Stored Procedures and select the SP:Recompile check box. Run Profiler to capture the metrics then review the results to see if your hunch is correct.
Here are some tips related to Profiler to help you get started:
If you are having a performance problem, check out the Performance Tuning category on the web site - http://www.mssqltips.com/category.asp?catid=9
Good luck and let us know if this works!
Thank you,
The MSSQLTips.com Team