madExcept thinks program is frozen when it clearly isn't

With the freeze timeout set at 60 seconds, the error comes up.  If I change it to 90 seconds it seems OK.  The confusing
thing is that the system has a TTimer running all the time, changing a banner to show the program is busy.  There is another thread doing all the work.  This is our security sub-system, so it is quite slow because of the complex encryption we use.  We decrypt three records, send them back to the client and then do the next three.

Is there a way to set the timeout higher in code and then after this, set it back to a lower setting.  Is there a problem with the main thread being quite and not realizing that a second thread is doing all the work?  I am just trying the product out and hoping to get some insight on the problem.