What specific dot version of PR?
There has been a bug if you are doing this in Adobe Media Encoder.
For a workaround or to test this, export from PR rather than queuing to AME.
Or, in AME preferences, set it to "Import sequences natively." If this was not set, you must reimport the sequence.
"Import sequences natively" was already ticked so that wasn't it, but exporting from PR solved the problem.
I have PP 12.1.2 and AME 18.104.22.168 which seem to be the latest ones so I guess the bug hasn't yet been fixed?
I had forgotten; right, not fixed. I am Win 10, and having "Import sequences natively" checked works for me (only if set before queued from PR or imported within AME).
That and export directly from PR are the workarounds. Glad one of them worked for you!
What OS are you running?