I have no idea about the finer points of Windows file permissioning. I haven't touched Windows in the better part of a month, and I haven't used it for anything serious in over half a year.

As for the code, if you have 1600+ lines, my suggestion is to try to write a small working snippet to test out what the module can and cannot do. The odds are reasonably good that your fundamental problem is somewhere else in the 1600+ lines, in which case what you have to do is to prove to yourself how that section is supposed to work, that it should work, and then trace backwards through, "If this is right coming into here then it will work correctly because..." until you find the mistake.

Don't debug the whole program at first. Write a small snippet, test it, and figure out how to make that work. Then work out from there.

Random tip. I've found with programs of that length that if they don't use strict.pm, then they often have several subtle bugs lurking where someone clearly meant to type in one variable name and accidentally typed another. This is common enough that I've found it a good strategy to add that and fix everything that it complains about. You'll probably fix several bugs pretty easily, and the one that you are working on may be among them...