In Mavericks, I was able to scroll through PDFs in Skim by pressing the up/down arrow keys, with the down arrow navigating to later pages in the document, and the up arrow navigating to earlier pages. In Yosemite, it appears that the up and down arrow keys have reversed when viewing a document in either "single page" or "two pages" mode (not continuous); now, the up arrow goes to later pages, and the down arrow to earlier pages. Is this a Skim-only change, or is the change more system-wide? If it's system-wide, is there a way to change it back to the Mavericks behavior?
Edit: It seems that some people aren't able to reproduce this, so it might be a particular choice of settings that is causing this strange behavior.