Thanks for the suggestion!
I think I did what you're suggesting though, let me make sure. I first downloaded the factory image from the radio, and I set up my local repeaters, then uploaded it back to the radio. Then I learned about the squelch thing, so I downloaded my file from my radio again, made the changes to the squelch, and saved and re-uploaded that file. After that, I downloaded the file from the radio again and it had gone back to the original squelch settings. It holds all of my repeater settings, but for some reason it won't hold the squelch settings. I can download the file, make the changes, and upload it back to the radio over and over. Every time I download the file back from the radio, it's gone back to the old squelch settings.