ALT2GXB loopback problem

This is your problem. Your transmitter is using the reference clock to create it's serial transmit clock. This clock is not the same frequency as your recovered receive clock. You therefore get an overrun or underrun from the transmit compensation FIFO.

The Stratix II GX and Arria GX do not allow you to use the recovered receive clock as the reference clock for transmit. You cannot do internal RX to TX loopback unless you are manually adjusting the reference clock to match the receive clock.

Jake