Frankly there's not a lot we can go off of to help you based on what you've told us. But, there are two likely issues. One, you accidentally messed up something in the .ini, and you should double check to make sure. Two, some of the ROM's data has been corrupted somehow (in which case you should re-trace your steps and figure out if you did anything easily reversible). Of course a third issue would be a problem with the program itself, but this is unlikely.
I resolved the issue. It seemed to not be an issue with any of the things I mentioned. It's a peculiar thing that happens only with this program. If I have opened another program, for example AdvanceMap and am editing the ROM, it won't open. And since I have AdvanceMap open and editing pretty much the whole time I'm rom hacking, I never thought it would be a problem. It's a great tool that's working like a charm.