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*headdesk*
Okay, if your setup uses a fuel injector relay to control battery power to your fuel injectors, then that behavior is normal. The code is detecting the pulse caused by applying power to your injector circuit, but the rationality checks are rejecting the pulse.
I think instead that I will just revert the injector interrupt code to use both INT0 and INT1 again, like the original 0.86 code did. It might be that one of your AtMega's pins is not as good as detecting signal changes as the other. We'll test that, instead.
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