It's apparently normal for the romtool dumps to change, but I never trusted them due to that. I've done the dump/mod/flash but never used a CH341A programmer. If the software for the CH341A can verify the EEPROM ID before flashing, that would be a good start, as it would help to ensure proper communication with the chip. Likewise, I assume the software can verify the EEPROM after it programs it. which you should also do. If there was a bad connection when you copied the EEPROM with the CH341A, then your romtool backups would probably be usable.
You could look at both in a hex editor (or use diff) and see if the romtool and CH341A backups are significantly different, keeping in mind that there will be some differences, as that is apparently normal when dumping with romtool. If I were doing it, I'd probably use Hex Fiend, then open both a romtool dump and a CH341A dump at the same time, then use the comparison feature under the File menu, which allows you to do a side-by-side comparison.
Other than that, I'd suggest you try an NVRAM reset, if you haven't already, as well as a SMC reset (which I think removing the button battery and then putting it back in will do the job on an iMac).
You can send me your modified ROM if you wish and I will check over it for you. PM me, don't publish it publicly.