Are you playing with the boot ROM active?
The boot ROM will require the header checksum to be correct. Though it doesn't care if the full game checksum is correct.
Apparently your emulator does. (and a FPGA is still an emulator as far as I'm concerned, technical hair splits aside)
Well, the header checksum is easy enough to fix anyways with a calculator (Windows Calculator can do that, just choose Programmer mode) and hex editor.
Off hand, I think the header starts at ROM $134 and the header compliment is at $14C.
That header compliment is what needs to be fixed, and to calculate, you need to add all the bytes before it in the header. You can add them up in a calculator, and then you need to only worry about the last byte (the two lowest digits). If those last digits aren't 00, then you need to do (hexadecimal) 100 minus that result to get the correct compliment value.
As the last poster said, you can make an IPS of the XDelta patch yourself. If you apply the xdelta patch to the correct ROM, and then use an IPS patch maker to create a patch yourself between the result and original ROMs.
But don't always expect that any two patches are necessarily going to work together. My advice is only how to get the two patches applied to the same ROM. No guarantee the result will be a properly functioning game.