Christopher Rooney

Thanks! I didn't realize this was the same bug as the "document scrolls when selecting text" and others since I hadn't noticed those behaviors. I found the hidden preferences page, but WhenScrolling is not listed as an allowed option for the AppleShowScrollBars. Nevertheless, using defaults write -app Skim AppleShowScrollBars -string WhenScrolling did the trick! https://sourceforge.net/p/skim-app/wiki/Hidden_Preferences/#h-system-overrides

Scrolling slowly with external mouse moves document in wrong direction