I found a very old thread with the Mac equivalent of Mark's recommendation for the kinoma folders. I wish I had seen this thread a few weeks ago. I had the disappearing Mac window issue in this link too. To fix it I uninstalled and reinstalled the software, which meant I had to reload my library and create my collections over. Wish I had known there was a simpler fix... However, the issue that you describe is different than the one that I had. You at least can get the software open, and it sounds as if your problem only occurs once the ereader is connected via USB.
https://www.mobileread.com/forums/showthread.php?t=59980