Long ago, I accidentally introduced a bug in the way JabRef stores the user-specific file directory setting in BibTeX files. If the user-specific path is set, JabRef introduces an @ character in the setting.
This is not allowed in BibTeX and causes BibTeX to cough errors on compilation of the bibliography.
I plan to fix this very soon.
Seems identical to bug report #1150
(https://sourceforge.net/p/jabref/bugs/1150/)
I have fixed the bugs 1153 and 1150 (duplicates) that I originally
introduced a long time ago. Retained (read) handling of legacy setting
containing the problematic '@'. To get rid of the setting containing
'@', users must manually remove this line from their database file. The
latter is not a bug but an intended feature.
Seems to be indeed fixed (at least in the current development version).