I managed to re-play from the beginning using new GeForce drivers. Just arrived in level 15 and it seems to work so far!
I uploaded my new savegames here:
I would be glad if somebody who previously had trouble playing level 15 could report that the new start_15_MACHINE.nds savegame solves the problem ...
Update: Yes - level 15 completely worked! I hope it does for you as well... I also updated the Aetherium and Peru savegames so the collection is now complete. Note that currently all the other files below ftp://ftp.soulianis.com/archive/indy/ still base on my older savegames and probably won't work for everybody.