Like Andy, this happened to me ONCE, on a bone-stock M5 after about 8K miles. I didn't at the time think to 'reboot' and turn on/off the ignition. Instead, I had the car flat-bedded to the dealership where (1) they couldn't replicate the problem, and (2) the diagnostic read: cylinder misfire. I have not experienced this fault since.
Since this appears to happen to non-modified M5s as well, it's unfortunate your dealership is responding as they are. As Jim says, that's one of the risks of modifying our Beasts (or at least doing so outside the dealership).
There are, however, a number of "aftermarket-friendly" dealerships out there that won't try to screw you just b/c you've got mods. I've found Hank Aaron BMW in Atlanta to reasonable and fair in that regard. Perhaps you could try working with another dealer?
Good luck.
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