I have also noticed a change to middle mouse button pasting in Fedora 20.
The middle mouse button used to paste into gvim at the position of the
cursor regardless of where I clicked.
Now, all of a sudden, it moves the cursor then inserts text (Yuck!)
I am using fluxbox as my window manager.
What window manager or desktop environment are you using?
The only recent and relevant update I see in /var/log/yum.log is ibus-libs.