I know this is late, but I'd like to at least explain what I think is going on. When you click on the mods button, the game does a preliminary check to make sure that all of the mods in your list are still working, and it does this by manually testing each mod to make sure nothing is malformed. This of course takes more and more time as more mods are added to your list, so if you have a large number of mods it's not unusual for Cosmoteer to stop responding. The "problem" is really just windows being trigger happy if you interact with the not responding window, killing the task when it's not really needed; simply waiting a little while should give Cosmoteer enough time to finish checking all of the mods, and then you can tweak them as normal.
If you're interested in improving the loading time, remove the mods you don't use anymore regularly, and keep in mind that bigger mods like ABH take significantly longer to 'load' than tiny things like Cosmofine
