Thanks for the reply.
IF a multimeter were available, the next test would be to unplug the regulator harness from the alternator. Measure the resistance from the Battery Sense terminal to the GENCOM terminal, (on the alternator, Not the harness). Must read 950 to 1050 ohms.
If it were even borderline close to being out of range I'd suggest another alternator.
The other possibilities would be that small 2 pin connector that clips into the alternator may have a bad connection or broken wire. Again, if a multimeter was available we could test those 2 wires back to the PCM and confirm they are ok.
Just a quick edit: even though your alternator IS charging it may be possible that this connector may be damaged still, it was common in the earlier 5.4 and 4.6 motors
Your question caught my eye because I've had an experience just like yours with a bad aftermarket alternator. Even if you believe the brand is reputable, my suggestion would be to exchange it for another brand. It would be a quick rule out of one possibility.
Let me know which direction you choose to go and please feel free to ask any questions you may have. Also don't hesitate to ask for any clarification if needed. Again, I look forward to helping resolve your concern and thanks for you question