Has Arrow Key Navigation Changed for Skim in Yosemite?
According to the author of Skim, there is a bug in Yosemite that swapped the up and down arrow keys. Some versions of Skim had the fix, and the author later decided to remove it. In the newest version of Skim, 1.4.12, the author re-added the workaround. From the changelog:

Reinsert workaround for Page Up/Page Down bug Apple refuses to fix