Ok -here's what's going on
1) Altera does support Vita57.1 for FMC. However, your card is uses the "user-definable" pins. Altera did a somewhat arbitrary assignment of their (non-bidirectional) LVDS signals to these user-definable pins, and in some cases didn't match the direction used in your card (did you follow any informal standard?). FWIW - I think if you had used the M2C/C2M pins there would have been no problem. I haven't checked Xilinx docs, but based on your prior statement I assume it's no problem with Xilinx because their LVDS are bi-dir and so can deal with any config of those pins.
I'm still out of luck, because we can't use your board with the card we want, and that Xilinx card isn't quite shipping yet (sigh).
Thanks for all your help though. I do appreciate it.
/j