Yeah, unfortunately the whole thing is pretty buggy. This being because I'm compiling it on the realitevely old .NET 2003 thing. I can't get Vista to accept the 3.5 framework (or the 3.0 one for that matter), and can't install the 2008 version. So, I get all kinds of glitches with people who, unlike me, update their OS.
The "Index outside of bounds" is because of the darn progress bar. No matter what I tried, it keeps accumulating integer convertion inaccuracies and after processing a very large module (like the Megamagic weapons ends up being - I'm not sure how large it is, but I'm suspecting up to a five-digit number of entries, depending on other installed mods as well) it tries to set the progressbar some 20 or 30 above its actual maximum. At least I think that's what causes it for most people, other variants can include mistreatment of the conditional tags, but that's a modder's problem.
The "Startindex cannot be less than zero" is something I haven't seen, but it's probably a case of the same mistreatment, because there might be little quirks in the syntax you don't know about.