I think you're misinterpreting what you see. The best way to look at this is to use the PHDLogViewer tool with two views. The first shows the native tracking error which usually shows the characteristic sine-wave of periodic error:
If you're just looking at this in real-time, you can't know the phase of the curve at the point you started the GA run. So the "zero point" for the GA graph can fall anywhere along the sine wave curve, there's no way for you to know. None of this shows anything useful about balance and the curve here is pretty typical for your type of mount. The second useful view is the frequency/period analysis which looks like this:
You can see your tracking is dominated by a 10 arc-sec peak-peak error with a period of 162 seconds. You can attack this by using a periodic error correction curve generator app like PemPro or you can use the PHD2 predictive periodic error algorithm for RA. For the latter, set a period length of 160 seconds and un-check the box for 'auto-adjust'.
Good luck,
Bruce