If you had old save files that were made with an earlier version, newer versions may crash when loading the old layer sets. Thats the nature of in-development software sometimes, I'm sorry that happened. If you send me the old layer set file, i can try to fix it for you.
The config file saves the last layer set you used and tries to load it the next time the app is run, so if something in your layer set triggered a crash it would keep happening until you delete config.xml
I'll look at that layer set and find the crash if you like.