All of the 2nd-gen CRXes, as far as I know, will "turn off" the alternator after the car has been driving a while. It is in the factory manuals, and I can see the system voltage drop to ~12.6 after a drive.
It is related to temperature (probably coolant temp) and the electrical load on the system as measured by the ELD (electrical load device or something like that), and probably to other things. If I turn my lights on, or the rear defroster, or even turn the cooling fan on speed 2 (with 1 the slowest and 4 the fastest) the voltage will go back up to 14-ish.
-soD
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