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.
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