Greetings,
It's nice to know that someone actually enjoying this mod. I made it just for fun because I thought it would be hilarious if sipedeys carry fruits on Gleba back and forth in my save.
Multiple dropzones would not do anything in your case, the script behind this mod only counts the latest placed one, so once you place new zone all previous become nothing but pure decorations. Same goes if you remove active station, it won't "remember" previous ones and would just wait until you place new.
Drop / load zone is just an [X, Y] marker (top left corner of an entity) which spidertrons are sent back and forth between. Every second script checks if designated spidertron is at [X +-5, Y+-5] and if it is there, either turns logistics on or dumps all inventory into trach slots. I guess your problem is that in most cases spidertron just does not detect that +-5 range and "think" it if not arrived yet.
What we can do:
1) You remove half of legs and give them to another spidey, because even when multiple stations do not count, you can still place multiple spidertrons on the same route perfectly fine
2) Next update I would introduce a setting that would allow you to select the "activation range" and make it 5, 10, 15, 20 cells radius so spidey would have more than enough room to brake.
Hope this helps