Keep us informed, Brett. A good part of my career has been involved in the care and feeding of itty bitty headless embedded systems (like, for example, timers and ESCs, although I haven't specifically done either of those). So I may have some insights to add along with yours. Life gets hard when they start doing intermittent odd things.
If you have an event and you report it to Brett, be sure to report on your whole setup: ESC brand and model, software version if you know it, timer ditto, motor brand and model, battery brand and model, connector brand and model, whether you use an arming plug and how it's mounted, how long your wires are from battery to ESC, ESC to timer and ESC to motor, how things are mounted, etc. In other words -- everything. Pictures wouldn't hurt. Also detail about what you were doing: where you were in the flight, what maneuver you were doing, whether it was cold, hot, windy, calm, humid, dry, etc.
Note if there are any "beeps" from the plane, too -- in particular an "I've just woken up and I'm happy" beep or a "hey, my receiver just crapped out" beep will narrow things down considerably.
If you have an ESC that logs events and the means to download it, by all means suck that puppy dry and see what it has to say for itself. That's your "black box" and should provide quite a bit more information than the indirect info available above.
If you're enough of an electronics geek to have a logic pulse detector in your tool kit and if you can do so without damage to yourself, check for pulses out of the timer, while you're at it.
Once the problem is figured out all that detail will seem excessive -- but you never know what seemingly insignificant detail is the one that means something.
Brett: how do you want folks to report in? Since I feel I have something to add I'd like folks to report to this thread, where I can keep tabs on it. But it's your baby.