Very strange! I started a new game, with just Alien Biomes + AB Graphics + Maps active. Cheated me an atomic bomb and a rocket launcher, looked for a forest and nuked it. I could just run over maps (small, normal, and big maps), so they were automatically picked up, but I also could select the items on the ground and pick them up manually. Everything was normal. So, has the issue been silently solved since you reported your crash?
Would you mind trying to reproduce the problem? A saved game where that still happens would definitely help!