If your Squeak VM is acting weird, you may have changed some settings on accident. To change these settings back, click on the Luckode clover at the top-left of the title bar or right-click the title bar itself.
Click on or hover over the VM Preferences dropdown. The options are sorted into categories.
Mouse mapping - If your mouse clicks are weird, you may want to set both the 1 button mouse and 3 button mouse options off.
Security settings - Allow file access - If files won't show up in file chooser dialogs, turn this option on. You may have to click Yes on a couple of dialogs.
Debug options - Show output console - If you have a weird white block at the bottom of your Luckode window, you may want to turn this option off unless you're debugging the VM.