Sorry for the lack of response this past month; I believe I know both of the issues you're running into.
Starting with the first issue, I'm fairly certain it's a long running problem with base game Factorio, which apparently still hasn't been solved. The Map Settings (at least for mods) don't seem to do anything if you try to change them on an existing save, without some... finnagling. I've tested this myself, by loading up the map, disabling the setting (which has no effect), then saving the game, loading back into the game, and the setting is back to being enabled. This has been an issue for at least... 4 years, according to this Reddit post: https://www.reddit.com/r/factorio/comments/bumkti/mod_settings_map_settings/
That was a rather annoying issue to debug... After a lot of testing... it seems like part of my problems (may not apply to you) involved having the "Use different mod settings per save" enabled, under the vanilla "Other settings" page; I could not get a single map-setting change to stick at all, for any mod. But even after having that disabled, it still wouldn't have any effect, just as you mentioned, and required loading up the save, changing the setting, saving the game, re-loading into that save.
However... I can't exactly test for sure, but I don't think this issue is specific to my mod... I currently don't have any other mods with map-settings, but I wouldn't be surprised if they all had this issue.
Onto your second (and more pertinent) issue... I'm pretty sure I set the logic for this setting to check on a timer (the ingredient push delay) if there was a recipe with not enough ingredients, and to push it to the output if there was not enough input. The problem being, that even if the belt is saturated, it might still check on a tick when the first part of the recipe has gone in (from the loader), but the second ingredient has not (even though it would be there on the next tick of the blue belt), so it pushes to output.
If only one side of the belt is saturated, this could happen once every time the delay was reached, if there was only 1 ingredient at the time. Short-term solution for you would be to fill both sides of the belt (using something like a small 1-lane balancer), or to use stack inserters instead of loaders for the input (since they dump in as many as possible each time they activate, thus there would never be a time when there is only one part of the recipe, unless you were actually short on inputs.
I'm not entirely sure if I can tweak the logic to check how long it has been since an item was processed (since the game might not have a function to poll that info), instead of checking on a delay-based timer, but I will look into it, just in case.
