Maybe try adding "-n 200" to the plxeep.exe command line to extract an additional 200 bytes after the 68 bytes and compare what you get to the new firmware file.
Usage: PlxEep -l|-s file [-p chip[,rev]] [-d dev] [-w width] [-i] [-n bytes] [-v] Options: -l | -s Load (-l) file to EEPROM -OR- Save (-s) EEPROM to file file Specifies the file to load or save -p chip,rev Limits device selection to a specific PLX chip type. If revision provided, it further limits to a specific revision. -d dev Specifies device number to select -w width Specifies an EEPROM address width (1, 2, or 3) to override -i Ignore warnings & continue (e.g. EEPROM not detected) -n bytes Number of extra bytes (after PLX portion) to save to file -v Verbose output (for debugging purposes) -h or -? This help screen
I tried this. It said it was reading an 'extra' 200 bytes, and the extra bytes were all zeroes in the resultant file.
The initial 68 bytes are the same though.