Is it a public model?

Yes, but the groups issue only affects the editor.

If it is public, I can go in the editor for the model and try to replicate the issue.

http://mecabricks.com/en/models/X1k2qx4baE0
I am trying to move the Flex Tube 12M from the "Nigel" group to the "Data Station & Recharge Dock" group.

All sorted!

This bug may have been here for ever 😉

The issue was only happening with flexible parts. To explain, parts are added to the viewport asynchronously but with flexible pieces some of them require additional geometry files that need to be loaded from the server. However, the time these new files were loaded, other regular pieces had been added to the scene and because of a context error in the 'for' loop, the flexible pieces were added as a child of whatever group the for loop was at (generally the last one as it takes more time to download something than to go through 1000s of pieces).

Happy that I know use ECMAScript 6 now. I only had to use 'let' instead of 'var'. 3 letters making the whole difference. Took me an hour to find the bug though.

Bottom lines is that it now works fine.

Fantastic! Thank you so much!