The only thing that should affect the house percent other than the slider is if you change her slave status.
Freeing a slave sets her house to 60 and enslaving a girl sets her house to 100.
Other than that, the only time the house gets set by the code is in character creation.
Rebel does not get saved, it gets recalculated each time it is needed.
If you can get more details as to when it happens and in what buildings it happens, that would help narrow down your problem.
I just restarted, but it happens in both the first brothel and in my house. I change the house percentage, go to another page (doesn't matter whether I go to inventory, brothel list or next/previous girl), and when I get back, the percentage reset. Some girls have this happen, others do not.
For some girls, it always resets to 100, for others it resets to something else. One girl reset to 75, so I went digging in the saved game for her and into her girlsx file, and found:
saved game: House Value="50" Mod="75"
girlsx: House="60"
One of the girls where I can freely change the amount didn't have the Mod= part specified in the saved game. After changing the percentage and saving, it updates in the saved game to the new value, and doesn't get a Mod= component or anything.
So far, it seems like the value for Mod becomes the minimal percentage taken, so the value any changes to a lower value resets to. And it seems (so far) like only girls who have the Mod bit behind the House Value are affected.
I'll dig more tonight when I get back from work if you need any more details, but that's all I could find so far.