Hello ; Please check the package of the used component, bad package I think.. normally all pins moves together in the same package.

@wraadefects, Can you identify and post the link to the PCB Footprint (or a screenshot of it in the SHIFT+F Search Libraries tool)?

It's called HDR-M-2.54_1x1. It's the default 1 pad connector from the EELIB panel on the left of screen, not the search library. Cheers. 

Hmmmm. Sorry but I can't reproduce what you are experiencing in Chrome or Firefox.

I know, it's very strange. I've used this footprint many times with no issues. It happens if (and only if) the X-location is 19.1mm or 19.2mm, but only in this project. I can't reproduce it in other projects. I can "fix" the issue by moving everything at once to a different x location. Hopefully it's a one off and doesn't effect other people's projects.