One point that hasn't been made is how the current can be modulated. In a PWM you can do it through different ways. You can have a fixed pulse width and modulate the off time (or the inverse). You can can have a fixed frequency and modulate the ratio between on and off.
Further you can work at different current levels, specially if you are working at short pulse widths. Since you can work at a much higher current level.
My guess it that maybe the switching frequency isn't to high, but when you have a long off period it could appear as a low frequency strobe. Does any one have a scope?