What is "unknown software exception (0xc00000fd)" error and how to avoid it?

I believe that 0xc00000fd is a stack overflow exception (http://support.microsoft.com/kb/315937). Without seeing your script, it is hard to say for sure what is going wrong, but this sort of thing is generally caused by recursing too deeply. I would check your script for any recursive functions and make sure that they are exiting before reaching too great a depth.

It's possible you're actually allocating too much on the stack. I'm not familiar with AHK, but it's possible the compiler is allocating a large amount of data (probably local variables) on the stack, too. If you define a large number of (or a number of large) local variables, this could happen.

It's also possible that the stack/memory is somehow getting corrupted, although this seems less likely to be the case when using a scripting language. It might be more likely when accessing native API from a scripting language, depending on how that is done.

The last possiblity I'm going to suggest here is that you're calling some API and causing it to allocate a lot of stack space as well, possibly by passing in bad parameters. Again, without knowing more specifics (especially what it's doing when it hits that exception), it's hard to say for sure.

I can think of some other reasons, but they're even less likely.