Hi,
Your post does not state what is the result you get, and what you'd expect. Also you do not describe your setup detailed enough.
Anyway, I had a strange GX problem with Cyclone IV GX.
I instantiated an RX-only GX unit. I did follow the reset sequence recommendation, but could not see freqlocked signal to activate.
Finally I found out that if I instantiate TXRX GX and do not use TX path at all, the freqlocked signal behaved as documented.
If I remember correctly, Altera documentation says that diff-clk is mandatory if using GX blocks. You could probably tie one pin to ground through capacitor, or tie it to a voltage which is middle of input voltage swing. But the jitter performance might suffer.
If you connect the negative pin to ground, you can not configure the input *** diff (the positive input can never have voltage smaller than negative input).
BR, -Topi