This has happened the last three times I've done the end boss in the Shallow Seas. I'll defeat the end boss with my crew. A gold amount will appear over my avi. I'll get sent back to Barton. And my gold will not have gone up. )=
If you do not have donor status, the end gold reward often exceeds your gold cap.
And is then not granted.
Every case I've heard reported of this so far has wound up having that as the source. Even on "donor", if you've been busy farming you can still cap out without realizing it.
If you're convinced this is not the case, go to this thread in the z!Dis forum BEFORE end of day 11/14 and post your bug there in hopes it gets tallied in the current round of fixes. If you do not, nothing else will be done - this forum is not monitored by Gaia any longer.