Toad shouldn't take 2 clicks on the X to close it. You might get some prompts about saving editor contents, etc, but after that it should close. I'm not sure what's going on there.
How many connections do you have in your login window? For me, the login window in 13.3 opens instantly.
If you zip up and send me your user files folder, I'll take a look. You can send it to john.dorlon@quest.com. Click here for directions on how to find the correct folder to send.