I still can't say exactly what causes this, but I also notice that sometimes components shift (instead of rotate) when I update them. I think both are maybe attributable to pilot error of sorts. I think what I was doing was replacing (my project) library components that initially had come from the CS Vault with my own versions not tied to Vault and not noticing that the schlib symbols were not aligned the same. I then made other edits to my versions, but had older schematics that were out of sync with what previously had been a 'copy' of the CS Vault component (you can't actually copy them like other components) and was now a version not connected with Vault.
Or something like that - I've been going through libraries and purging anything that points back to Vault and updating components in new design revisions as I go along. As I do that I'm seeing this happen less and less.
IMHO this is yet another reason why the inability to compare a schematic & layout against the libraries leads to unexpected problems: Update a project with all component updates from multiple libraries