I suspect the source of the problem may be some internal fault in the voltage regulator that's causing it to intermittently shut down. Whether VVCS is enabled or disabled, the voltage regulator controls the alternator's output either by carrying out the ECM's command or by using it's own defined parameters if VVCS is disabled. However, the inputs for determining alternator output are different in each case. The input the ECM uses for the VVCS system is based on current draw from the battery via the signal it receives from the battery current sensor. The alternator's input when VVCS is disabled would be the voltage detected at the alternator S terminal. I think you've basically determined that regardless of the input, the alternator is intermittently not charging. It could be some problem with the B terminal wire that goes directly to the battery so definitely try to rule that out. I would suggest a voltage drop test on the positive side of the charging system if you can get to the B terminal (...connect DVOM leads to alternator B terminal and battery + terminal). Voltage drop should be no more than a couple of tenths. Jiggle the harness and see if the voltage jumps.