I have not used Jabref for quite a while ignoring it in favour of Endnote, Mendeley, Zotero, and Wizfolio.
Each of the four alternative worked well in their individual spheres and I am quite happy using them. However, if you work with complicated documents across workplaces and computers you soon realize that each one of them has their own peculiar limitations that one needs to take account of.
Endnote is in my office computer and in my windows machine and does a splendid job of cite while you write, managementn of citations and all that. It's a great software and I have been using it for the last twenty years or so, and it's just great. But I also work with bibtex and on linux and on these projects, endnote does not work.
As an option, I downloaded and used Mendeley for my Windows and Linux boxes. Mendeley works and plays well with Word and OpenOffice but it has this nasty habit of tripping up every now and then. It happened while I was working on this long big text and Mendeley did not connect to my OpenOffice. I removed Mendeley from OpenOffice.
That's when I started using Jabref over again. I am mighty pleased with it.It's robust, and works every time, and it's also very flexible.