I'm willing to take a look at the source if you'd like, although my grasp of VB is pretty basic (no pun intended.) I'm more of a C# kinda guy.
For the record, I noticed the format difference by doing a binary compare in UltraEdit-32, saw one file had a single-character linebreak (CR or LF) and the other had a twin-character linebreak (CR and LF.) From there it was a pretty short leap of logic.