Resurrecting this thread because I was just having a similar issue...
Problem - I had 'move by whole pixel' enabled, yet the arrow keys nudged elements by unusual amounts (I think 1.4 pixels).
Solution - In File > Document Setup I noticed the DPI was set to 192 DPI. Changed this to 72 DPI (as it's a website design) and elements now snap to whole pixels.
The document started life as an Adobe Illustrator file, must have set the DPI as 192 DPI when I imported it into Affinity Designer.
Hopefully this will help someone.