It sounds to me like you had a good system going, and I doubt your FPGAs are dead. Do you have a volt-meter that you could measure the output from your power supply with? If that looks good, it could be that the protection fuse on X6500 has blown. This fuse should only blow as a last resort, particularly if you supplied reverse voltage, so I don't know why it would blow in your case. Were you using the Molex connector or barrel connector? Each power input has it's own fuse so you could try using the other one (if you have a suitable supply) to figure out if the fuse is to blame. If it is, please send it back and I'll replace the fuse for free.

If you don't feel comfortable testing it, I'll gladly diagnose it for you if you send it back. If you're pretty handy, you could replace the fuse yourself or bypass it entirely (although you'll lose the protection it provided, of course). I'll email you the address to ship it to.

Sorry for the trouble!