I'm having a similar problem on OS X with XQuartz 2.7.2_rc1. From a
stackoverflow discussion, sending "pause mouse keypress" seems to make
the cursor coordinates update, but none of the mouse clicks ever get
accepted.
That a hint of an issue with recognizing mouse inputs between XQuartz
and gnuplot. I'll have to find some time to go back to older versions
of XQuartz to see if that resolves the issue.