I've worked on literally hundreds of alternators problems and I have never seen a case where an external regulator was incompatible with an alternator. Not to say that I just haven't seen them and they are out there but I am doubtful. An alternator may not operate right but it should be the same if it gets input to its field to turn off and on by a regulator. Alternators aren't really biased that I know of. In general, if an alternator can put out full juice then it should be able to do it with a properly functioning regulator.
If you can rule
out the alternator as being the problem then it is either wiring
or the regulator itself, as influenced by the batteries and other charging sources which can certainly make an impact. When testing an alternator you should turn off all other charge sources and make sure the battery has some juice drained off of it. A good regulator and good alternator should not produce a charge if the batteries are already topped off. One thing you should do is to make a note of voltages when you are checking any of this out as you may see different results at different battery voltages.
Always, always double check all the wiring - especially the itty bitty wires that go to the regulator. If you have battery and/or alternator temp sensors then disconnect them and see if it makes a difference too. They can be bad sometimes. And, check the big wires on the alternator. They vibrate and can come loose and give intermittent results (AND it could cause a fire which has happened. I replaced all the wiring in the engine room for a cruiser in Mexico
once for that. He was lucky he had just left the anchorage and we could race
out with dinks to bring him back in).
And someone mentioned that the speed of the engine could matter so try that. If you put on a lot of loads while checking and the alternator comes on that will bring down the battery voltage before the regulator starts the alternator, which it should do. On boats with microwaves, I would nuke a cup of water
for 60 sec and then try the alternator. That normally pulls the batteries down enough to cause the regulator to turn on the alternator (but not with huge banks - you would need to bring them down by other means). All said I would suspect the regulator if the alternator works at all.