I have this issue too. For example I have a textarea and when users use line breaks and click save it is all saved without the linebreaks. The nl2br would not assist in that situation since this is not yet outputting — it is instead just trying to save the original info.
I've just tested, I've used a custom field textarea field. The line breaks was saving fine and I can see the line breaks in the admin panel and in frontend edit post area too. So that should be working.
I have had this issue with various WPUF versions (not only wedevs version but also the original). I even hired an outside developer to help develop a customized version and this was one of the bugs I wanted him to fix. it does not happen all the time, but I estimate about 50% of the time it happens, so it is difficult to troubleshoot.
It usually seems to break when using Opera, though I have had issues also with Firefox. I have not seen the issue with IE or Maxthon.