I'm not sure if this is related to updates or not, but it's super annoying. Every now and then, when Firefox starts, it tries to open up my home page tab and a tab related to the extension, but then ditches them because finally in the startup process it realizes that it wasn't supposed to load those anyway, but was supposed to load my tabs from last time (Firefox is just stupid like that; awful, buggy, insecure piece-of-junk browser, but still beats the competition). In any case, I'm not sure why it's trying to load the extension page in the first place, as it's not even on my home page list, but when it does, if I go back to it later I'll see that all my non-default settings of any kind are lost.
If what FF is telling me is at all accurate, the extension was last updated 2018-04-21 to 3.0.4, but I've been experiencing this problem lately, not way back then.
I've started keeping all my custom filters in a separate text file and pasting them in whenever ABP forgets everything. Better typing them in a text file anyway, because the text box on the settings page is junk. But still really annoying to have to put my settings back where they were every few days.