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.