I have been having issues for freaking ages. Yesterday I came close to throwing my keyboard across the room. I did some decent investigating and found out that the URXVT perls copy/paste commands are the culprit.
I commented the following out of my
!URxvt.keysym.M-c: perl:clipboard:copy !URxvt.keysym.M-v: perl:clipboard:paste
and my copy/pasting woes are now a thing of the past