I have seen similar issues recently (very sensitive snapping, not… snappy snapping anymore). I suspect this happens when your try to align elements that are in the same section.
I had the same issue. This may help you.
You may have moved a collection of objects around, which may result in some frames being not perfectly aligned on the pixel grid. “Snap to pixel grid” does not mean snap to pixel grid in frame, it means snap to pixel grid in the ENTIRE page. So, ensure your frame is aligned to the pixel grid, then your align buttons will align objects properly to the pixel grid. Hope that helps!