Well fact is your maps are unchanged, i.e. EQ2MAP did not get installed to your active EQ2 install. And fact is further that the EQ2 that you linked to your EQ2MAP updater is crashing, whereas (I assume) the EQ2 your launch manually does not crash. Draw your own conclusion from it if you can, I gave you the only one that makes sense to me.
PS: Ignore the E: drive thing, that's not related to your install but rather the drive SOE compiled it on.