Ok nevermind. I could get the map and it worked like the automap should. The problem was me not using the right tool. That made me spot another problem tho, that also happens with usual doom iwads.
When you end a level with the glowing-eyes power, you start the next level with this power as the active "weapon", but the power as inactive. (no journal pages appearing, no golden view effect) And since it looks similar to the picking up things 'weapon" but can't actually grab things in that state, the confusion happened to me. :p
Maybe a good fix would be to make the player start the level with the picking up things "weapon" set on by default. ^^