Battery/Alternator Light On Even Though Battery Is Charging and Alt Checks Out

I've got a 2011 CVPI that had a failing alternator (66k miles, low idle hours,
pulley clutch was failing anyway, then it just stopped charging one day). I
purchased a re-manufactured alternator at Advance Auto and swapped it
out. Replacement alternator did not cure the battery light, and when bench-
tested, came up faulty, so they swapped it for another unit. Installed that and
battery light disappeared initially, but came back after a night of driving. I had
just replaced the battery before installing the replacement alternator and
made sure it was charged fully before trying it out. Battery terminals are
clean and properly installed. New alternator does check out in-spec with
13.52v no load, and 13.50v with load. This is the 200 amp police interceptor
alternator and I was used to seeing 14.2v before, but now I only see 13.5 (I
have an OBDII mini-display I'm using to keep an eye on system voltage
while I figure this out). Wires all look OK, but that doesn't mean there isn't
some sort of short somewhere, maybe in the com wires to the PCM?
Anybody have any suggestions?