This problem has been reported downstream and can be reproduced always following these steps:
http://bugs.gentoo.org/show_bug.cgi?id=306259#c6
1. Start a new document
2. Write "hi", highlight it, press ctrl+x
3. Hit enter once to create a second line
4. Leave the text cursor on the second line
5. Middle click the first line
6. Press ctrl+v
7. Notice how it's pasted on the top line instead of the one with the cursor

Thanks a lot for fixing this if possible :-)