Unless your reputation is low enough people have stopped talking to you, or it happens again, I'd suggest you simply ignore this bug. Unfortunately, I don't see any practical way to fix it.
There are several problems with trying to find the real reputation value;
[*] Other stuff is added or updated when a quest is solved, so the size of the data files change. The size difference makes it
much more complicated to look for changes between files, and I am not aware of a freeware program which can do so. Even with a very well designed payware program, it would take a fair amount of effort to isolate a specific single-byte change.
[*] Since reputation is a single byte value, there will be many matching instances of that value, most or all of which would have nothing to do with reputation. If the number were larger (like experience points late in the game) you could search for matches and check a few results by trial and error, but that is not practical in this case.
[*] The base reputation is stored in the story.* files (see below for description). While this makes things easier in that these files only keep track of quest information (a lot more things can change in the data.000 file), the size difference after a quest update would still make it hard to track down a specific change, and (unlike the data.000 file) there are no ASCII strings in the story files that could help in figuring out the data structure.
[*] Since the game is keeping track of individual NPCs' opinions of you separately and adds it to the base amount anyway, the game might not actually store the total base reputation value anywhere. When loading a save and reading the quest information, it could simply add up the individual amounts. It may also keep track of the base reputation with several variables, possibly associated with various factions, rather than per quest.
I loaded an old save before talking to Homer about killing the trolls (reputation 4, Homer's opinion 14, wife's opinion 4) and then talked to him to get a +3 bonus (base rep 7, Homer's opinion 67, wife's opinion 32). After copying the story files from before completing the quest into a copy of the save afterwards, the base reputation dropped to 4, Homer's opinion stayed at 67, and his wife's dropped to 4. I went over to the army barracks to get caught stealing (-10 penalty, so my base reputation was -6. Homer's opinion dropped to 4 (ie 14 minus 10), while his wife's opinion dropped to -6.
The fact that Homer's opinion was initially unchanged implies that a temporary (or display) value is stored in the data.000 file, but when the story files are updated, so are those values (so he lost the bonus from completing the troll quest). His wife's boosted opinion of me after completing the quests was not cached in the data.000 file because I had not talked to her yet at that point. If I talk to her, then save and replace the story files, her opinion stays at 32 (at least until the next quest log update).
In any case, your reputation does not matter much (as long as people will still talk to you). The merchants you trade with most often, or NPCs you help directly, are going to have a high opinion of you regardless of your base reputation.
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