Hi,
My board is back!

I changed to 12V connector and it works. On the 5 V molex which I used before no current gets pulled at all. Seems you are right, the fuse is gone. Don't know how this could have happend. I am using a standard PC power supply....
Maybee under 5V voltage drop? The current gets higher if the voltage drops and fuses are likely to burn?
Can you give me the position and data of the fuse? I can relace it by myself - less hassle comparing to sending the board back and forward through the customs...
Is it the part with the "w" on it?
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!