Yeah - reinstalling the software seemed to stop the unexpected crashes. The "unusable" files had actually simply been saved files with only the subtitles checked off. Once I went back in and checked the video and audio streams, everything worked fine. As usual, my problems were my own poor understanding of subler!
I've found that I can speed up my workflow by importing all episodes into one file (only importing the subtitles). It takes a long time to create the file (due to OCR) but, once it's done, I can simply select each stream and export it (remembering to change the name appropriately as it always defaults to the same). I can do subs for 23 episodes in one foul swoop!
I'm curious why Subler does this so well and easily. I had downloaded several other pieces of software to use OCR for converting VOBs and they were all very daunting (having to correct matrices and such). Are there other tools out there that simply take their best guess and produce something reasonable like this?