Flattening image results in uxepected pixel shifts or white squares

When merging all layers in an image to a single layer or background image (flatten image), inconsistently pixel shifts or white squares appear in the image.

This problem appear mainly in large images (for example: 300x60 cm @ 240 dpi)

Original layered image:

Image after flattening layers:

Since I cannot find similar problems on the support forum, my only solution for now is to downgrade to a previous, correctly working version of  PS.