I did a search and couldn't find anything about this, apologies if it is a dumb question.

I am using ArgDub's excellent tool to read and write my ECU's EEPROM in bootmode. I have my EEPROM image that I have altered to clone my immo, and fixed the checksums. After I wrote it in bootmode, I wanted to check and make sure the write was successful, so I read it in bootmode and via OBD2 just in case. Both times there are 4 bytes that differ from image I uploaded - 112H-115H is 7C A3 AC 69 on the EEPROM, and 8A 1B F7 FD in my image file. The checksums are still correct after reading the image as well.

Is this to be expected? Does anyone know what these bytes mean and why they would change?

It's most likely from when you are re-reading it via OBD. Since the ECU is fully powered up and not in bootmode, it's looking for sensors and other electronics that it isn't currently connected to. What you are seeing should just be a change in the DTCs that are stored between writing and re-reading over OBD. You can check this by writing via bootmode, powering off the ECU, and then re-reading it back over bootmode right after. The code should be the same.

100% correct. Writing with bootmode, powering off the ECU and then re-reading it with bootmode right after results in an identical file.

Also, noticed with the flash wiped (using Galletto to flash in bootmode, and it wipes and then fails to write one of my flash files, leaving the flash blank) I am unable to read or write the ECU EEPROM in bootmode because ArgDub's tool cannot automatically find the CSpin, and I didn't know what it was. Was freaking out a bit until I figured that out.

I have a multimeter, but I don't know how to do this. In any case it lists the CSpin for my EEPROM as P4.7 when it autodetects, so I know what it is now.