I would suggest double check access rights. Is that user allowed to change the reference? Also check for any OnChange actions on the form and check those.
How is this popup page opened? Using an open page button (or edit button) or via a microflow? I seem to remember having issues (especially in Mx6) where I had unanticipated behaviors when opening a popup page via an open page button. I got around these issues by creating a microflow that had an open page action in it to open a popup page.
Also, Ronald's suggestion is a good one: are there any before or after commit events on the entity?
One other suggestion to help troubleshoot: what happens if you open a page to edit this entity in a full page (i.e. not a popup)? Does the behavior change?
Hope that helps,