I'd bet the activation wire that feeds the fields in the altenator isn't getting power all the time..its a brown,tan,or white wire,the other red wire in the two prong plug also needs 12V present to turn the regulator on in order to charge..
I've seen that wire corrode into white dust anywhere from right at the plug itself,all the way to the fuse box,and it will look perfect from the outside!--it'll have one or two strands that make contact ocaisionally,and let it start charging,then they heat up and break the connection..where the wire goes into the fuse box can corrode too..also,the printed curcuit board in the dash is part of that wires circuit,(the "ALT" light)--so if that fails or has poor connections the alternator wont charge when no current gets to the field coil inside it..(trucks with voltmeters by pass the printed curciut,since they have no "ALT" lamp in the dash)...
More than one GM truck I owned had similar charging problems,--either they refused to charge at times,or I'd have to race the motor up to 3 grand to get the alternator to "kick in" and start charging!--and I replaced many alternators and batteries until I found the real trouble--the wiring harness going to the altenator(the 2 prong plug's wires)..
I ended up running a new wire with a #194 marker light bulb in line,for resistance,which is needed for it to charge right.(usually the "ALT" light in the dash was the resistance,or a resistor was used on voltmeter equipped trucks) I ran a new wire from another 12V source that is hot only when the key is "ON" to the alternator plug,with the #194 bulb inline,and it never acted up again!..
