There's rumblings out there that a lot of the R46 converters are bad, which means that the stop and go nature of the line isn't good for the 46s.
I'm skeptical of this rumor because they ran on the just fine until they was swapped to CI, also the 46s are SUBWAY cars, not some locomotive hauled diesel train on a commuter railroad.
Perhaps only the Pikin Yard 46s have bad converters, while the Jamaica/CI Yard units do not, who knows.