i don't see how i could make a more detailed bug report, i messed around testing things and the mod seems to be working perfectly other than the config options not being saved, always reverting to trauma for quality 0, ugh for 1, etc.

i'm sorry if this isn't particularly helpful, but it's the best i can do.

i tested it with just this mod, this mod's api and mod config menu pure, and the config options still would not save. i've had issues with mod config menu pure not saving configs in the past, though i believe it was just for the config menu's own config options.

nothing particularly noteworthy appeared in log.txt, not even any warnings for this mod or its api.

The fact is that, I've tested with other mods and my settings persist, wheter they are the true or false ones or the reaction ones.
If you go into the local files (by going on the steam library -> The Binding Of Isaac -> Cogwheel Icon -> Manage -> Browse Local Files) you should see a data folder.
Is there a reaction_port_pack folder in there?
if not then that means that the settings are not being saved at all, otherwise it means that the settings are not being loaded.

the folder is there, and it has a save2.dat file (and i have been using my second file)
is it possible that the mod is only checking for the first save file?

No, mods should not have that capability, it uses the save for the respective save file you are currently using, just as a final question if you open the file with a text editor, is the data correct or wrong?, note that some settings are saved as numbers and not as text, so if you see that it is perfectly normal

it doesn't seem to be correct, though i may be misinterpreting it. one thing i can see is that despite me disabling the ugh sound effect, the ugh reaction still has it selected, so that seems to be enough confirmation that it's not being saved properly.

Ok, so the data you see is what is actually being loaded? if that's the case then the settings are being saved incorrectly.
As a final request (sorry if I'm bothering you) can you try and modify the settings for everything at random and see if they also go back to default.
Also when you close the game do you see Any ERROR, be it from my mod or from another one?

Ok I'm having the same problem on the second file, I will be working on a fix soon

you're not bothering me at all, i actually really appreciate your help!
changing the values randomly didn't work either unfortunately, and in fact the file itself reverted to the default settings.
the only errors i've had were from gfx files not unloading properly, but that was even happening when it was just the three mods i tested.

oh, i see! that's very strange, but i'm glad the issue has been found!

It seems I misunderstood how save files worked in Isaac, it actually copies the savedata from the 1st file like you said, and since it didn't find it reverted to default

ohhh, that actually makes sense in a way. so if i set up the options on save file 1 it would affect 2 and 3?

alright i went ahead and tested it, and setting it up for file 1 does seem to affect the other files, so i won't have to change it on every launch after all, which is a very pleasant surprise.
thank you so much for all your help, and sorry for taking up so much of your time! i'm glad this is (at least for the most part) figured out now.
i'm not confident in there being a way to get it to save to and read from the correct save file, but it's not a big deal either way.

I made the mistake of loading the save files on game startup, so it always defaulted to file 1 whilst I should have loaded them when someone starts a new/continued run, where the game can properly determine what save to use

FIXED - Now you can have different settings for each Save.
You can even switch saves without reloading the game and the respective settings will be applied

The reaction track doesn't switch back to the stage music when you pick up the item or it disappears while the mod is used with the Soundtrack Menu.