This (or something similar) occurs in the current version for me. I notice it most when I place down a blueprint. The lane filter flag is the opposite of what I the blueprint has.
I have read into the code abit, it seems the problem is caused by the mod (alongside the always output full stacks one) will attempt to toggle the "mode" of the loader whenever it is placed, be it from inventory or as a blueprint, if you have the option to toggle the default enabled as your per-player settings. Turning that option off will stop the loader settings from getting flipped when you pasted down a blueprint.
One way to fix this would be for the mod author is to create a new fake type of entity and replace the item placement result and then have it (and only the fake entity) replaced by an appropriate type of loader depending on your settings, so that the replacement code is not run when you are pasting a blueprint which would already be the entity that has the settings applied.