Branch,
I would take Semp's advice.  I had the same problem.  It seemed to occur at the absolute worst times.  It happened so often that I had the "Chilli fix" down pat (unplug the connector to the stick or throttle and plug back in).
All of the buttons would respond appropriately after reconnected.  Then I took the advice to use the USB hub to connect to the computer and haven't had a single recurrence.  It has been a week.
Good luck sir and let us know how it goes.  I was lucky that I had a couple of hubs sitting around not currently in use.  
Now, Semp, this is the curious thing.  The Hub I am using now, does not have an external power connection.  Still, it has solved my problems.