First thing I usually do is to check the event log. If there's any errors related to this issue, fix it. If nothing useful can be found in the event log, try performance monitor and see if you can get any clue there. Another thing I always do is to apply all the available updates to the server, especially if there's a problem. If nothing helps, move the application to another server and figure out what really causes the problem, the file server or the application? This particular type of issue, network monitor might be helpful as well.
Just my troubleshooting steps.
Just my troubleshooting steps.