Well, I'm still fighting this problem but hopefully I can overcome it soon.
Vaughn,
Keep up the fight, mate, you'll get there in the end.
... with over 5000 modules ...
That just could be the problem, and e-Sword could be struggling with that very issue and is dropping some files. I dunno for sure as that is just a stab in the dark, but might be worth looking into. Also, I concur with what both Josh and Jonathon shared as well.
Blessings,