Hi,
I had almost the same issue as you.
You can use a different clock at the output of the fifo, but it has to have exactly the same frequency (which is the case if you use the rx_clkout of gxb1 to feed gxb2).
And you have to tell quartus that both clock have the same frequency (GXB_0PPM_CORE_CLOCK property). I was trying for quite a time until I found the correct syntax.
Try this:
set_instance_assignment -name GXB_0PPM_CORE_CLOCK ON -from "fiber_trx_lev1_aria2gx:Fiber_Lev1_Left|rx_clkout[0]" -to {the serial input port of your top level design[0]}
set_instance_assignment -name GXB_0PPM_CORE_CLOCK ON -from "fiber_trx_lev1_aria2gx:Fiber_Lev1_Left|rx_clkout[0]" -to {the serial input port of your top level design[1]}
(maybe you need to adapt the command a bit)
The strange thing for me is that in the "-to" field you need to assign the serial input port which comes at a much higher rate. But I got it working this way.
See
http://www.alteraforum.com/forum/showthread.php?t=21970 for my configuration.
Cheers.