I had the same issue. What I did to resolve this issue was change the compress save files setting in game. I believe it's found in Settings --> General at the bottom of the screen. It should then leave all the save files in .xml format after you exit the game.
Sorry for the late response but I unfortunately don't have any idea how to modify faction relations. When it comes to those type of tweaks, I tend to stay away from them because of the uncertainty around the specifics of the number. The only solution I can give is make a quick backup of the save then tweak the faction you want to improve. Then in game see if there is any change and if not revert back to your backup. Sorry I can't give a better solution but I hope that helps.
Was just posting to change the reputation. Open save file in notepad++(what i use)
step 1. search for faction id="(insert faction name all lower case)"
example faction id="plutarch"
step 2. go down to the line
step 3. make it look like this:
booster faction="player" relation="0.1" time="13811.753"/>
remove the - sign
i was able to change the faction standing to a plus 20 instead of - 20
In my notepad++ the line the change is made on is line 469 for plutarch.
Do you open a shortcut you created to the Save Game Editor? Have you checked the related application in the Properties?