I would strongly recommend you replace both batteries completely, whether or not they hold a charge. Don't forget, if you loose the engine, you can land, but if your battery goes, "That's all for now, folks".
I normally replace mine every three or four years just to be safe.
As for your problem, I had a similar situation a few months ago. Batteries checked out, crystal was good in both the transmitter and receiver, and all the wires were good. It turns out that the antenna had failed at the solder joint, so all I would get was a glitch at startup. You could also have a faulty wire somewhere - try bypassing the battery straight to the receiver; remove the switch harness all-together to eliminate that as a cause. If nothing still works, try wiggling the plugs a bit - this could reveal a loose wire as well.
Hope this helps,