I´m struggling to understand how this could occur, and I´ve certainly never seen it before.
Can I ask:
Are you on the leatest version? This could ceratinly explain it, long answer upgrade to the latest version.
Are you sharing the taxonony across other objects other than users? This could ceratinly explain it, long answer don´t do it.
Have you specified a update_callback when you registered the taxonony? This could ceratinly explain it. Not sure why you would do that though.
Finally if any of the above are not valid leads, then are you getting any errors in your debug log when you add a term in the client taxonomy to a user?
Pete
I am closing this thread for good order but will still
Monitor it and if necessary reopen it.