[JabRef version 3.8~pre2+ds-1 from Debian/experimental. But the issue is not specific to this version.]

The X Window System has usually three "selections": primary/XA_PRIMARY - copying by highlighting with the first mouse button, pasting by clicking the third (middle) button; secondary/XA_SECONDARY (never seen this in action); and clipboard/XA_CLIPBOARD which acts like the clipboard on e.g. Windows (Ctrl-C, Ctrl-V and copy/paste menu items or buttons).

It seems that JabRef only supports the last version (the "clipboard"). This can be seen e.g.

• in the "Copy DOI URL" function which copies the URL into the XA_CLIPBOARD selection (and not (also) into XA_PRIMARY);
• in the "New entry from plain text" dialog, where (first of all neither middle-clicking/XA_PRIMARY nor Ctrl-V/XA_CLIPBOARD in the text box does anything but) using the "Paste" button pastes the contents of the XA_CLIPBOARD selection.

I don't know how to make Java under X11 use the XA_PRIMARY selection as well but I'm sure this is not the first time in the history of Java that this question comes up :)

Cheers,
gregor