I can tell you now exactly why that's happening - it's related to the trigger area overwrite issues in original Lemmix / DOS (for example, how a trap's trigger area, or a blocker, could cancel out steel). In NeoLemmix, this is somewhat avoided by having four seperate planes of trigger areas, but this can still result in overlap between trigger types on the same plane. I might move pickup skills to a different one...
For reference, the four planes are:
Plane 1 - Zombies (and nothing else)
Plane 2 - Steel and one-way arrows
Plane 3 - Blocker fields
Plane 4 - Everything else
I don't want to add too many planes, as it could eventually have performance impacts (especially on larger maps), so I might see if there's some other workaround for this I can come up with.