Hi Reg,
Double check your jumper settings before you try anything else... A14 Select and A15 Select need to be un-jumpered to use a 28C64, and ROM_EN needs to short pins 1 and 2 to enable the ROM chip. The way the board is laid out can make this non-obvious at first.
Make sure your ROM chip is good by reading it back and comparing the dump file with the file you wrote. I seem to remember that the EEPROM programmer you have has a "detection mode," so you can tell it to look for a specific chip (in this case, 28C64) to make sure you bought the part you think you did.
If that doesn't uncover the problem, give more details... what specific CPU are you using, what clock speed, etc. I found the SBC version to be a bit fussy to get working, but I did eventually find success. (My modular backplane version is zooming along at 8Mhz with a modern WDC 65c02.
Edit: Hey, rereading your first post, I think maybe I misinterpreted your question. You're having trouble getting the ROM to work with the programmer, not with the SBC, is that right? In that case I'd suggest abandoning the manufactured software and switching to "MiniPro:"
https://gitlab.com/DavidGriffith/minipro/. I run it on an old ThinkPad with ubuntu; there's also a MacOS version. Not sure if there's one for Windows.