Thanks guys, there must be something else going on. I incorrectly mentioned above that the PHD2 pulsing was mostly West, when in fact it has been mostly East. I don't think the direction matters though. I agree it has something to do with the PA, but other than that setting, my PA has always been the same process every time since April.
I imagine an imbalance in RA would cause this to happen as well, correct? I normally do not balance East heavy in RA or camera-end heavy in Dec. I try to have everything just well-balanced, so I wonder if I have gotten loose in my balancing routine.
One more thing I found out which is odd. The last couple of times where I saw this, I did a recalibration and found that the RA & Dec axes PHD2 calculation were not 90 degs! I'll have to get the logs to see how far it was off. It had always been almost perfectly 90 degs every time before then, with no perceptible backlash. Again, I imagine these two are related. Would you guys agree these are related?