It looks as though there's a known issue with the Profile:Edit addon not saving custom fields. That could be the culprit.
There’s a problem caused by the 2.5.4 update. Specifically, safecracker entry submissions will partially fail, resulting in custom fields not getting filled in.
Problem is mod.profile.php at line 878 - the exp_security_hashes has changed in structure and no longer has an ip_address column.
Turning off Secure Forms is a workaround.
Disabling secure form processing is generally a bad idea, but it's worth a try in your dev environment so you can verify whether that's the problem. If it is then you'll probably have to wait for a fix to be released.