I tested on a loaded profile (multiple filter lists; lots of other extensions), and also a fresh profile, newly installed ABL with just EasyList (no other extensions). Nothing got disabled.
I don't know why your filters were disabled.
Presumably you either disabled them yourself and forgot (that happens more than people like to think), or (rare) they were disabled by an anti-adblock script on some site (I believe I've seen this occur once). If some other reason is possible, it's not one I'm personally familiar with.
Have you tried making a copy of your portable version, and testing updating ABL with that?
If you care to know which filters were disabled, open the Filter Preferences as mentioned earlier and sort on the Enabled column in the right-hand pane.
After rolling back, you might need to restart the browser to restore the toolbar button.
(Be aware for the future that 4.0* won't be compatible with Pale Moon on the uxp platform: Pale Moon 28.)