Ah... that would explain it.
I must correct myself. I have the left shift in all PAL games, no matter if WHDLoad or NON-WHDLoad.
As it happens, I had already noticed and taken care of the sync inversion with V1 hardware.
I think the problem you're seeing happens with system-friendly games that open a low-res screen?
Also DPaint / PPaint show it too, if you open a 320x256 screen - but are OK if you open a 640x256 screen?
As a temporary workaround, use overscan prefs to set PAL overscan to its minimum width and rightmost position.