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.