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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.

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    LOL. Changed the settings, no effect. Closed the application, reopened it and now it is doing exactly what you said. Up goes down, down goes up. – Alistair McMillan Oct 18 '14 at 11:12
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    I have the same problem. I use "Space" for next page, so I was very surprised when it started going backwards. In "Single Page Continues" it scroll in the right direction. – Boklucius Oct 18 '14 at 21:33
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    I can confirm the same Effect - since updating to Yosemite Skim keys for next/prev. Page are reversed. I deleted all preference files for skim but had no luck so far identifying the problem. – J.C. Oct 29 '14 at 20:09
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    Same here. Horrific since I'm doing my first Beamer slides since updating OS. – Jimi Oke Nov 8 '14 at 10:22
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    By now you've likely noticed it has been fixed. It was a bug that continues in Yosemite and the Skim author was hesitant to include a workaround. It is now in the current version of Skim. – empedocle Jul 7 '15 at 15:26
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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
  • Skim 1.4.12 must have removed support - PgUp/PgDown are again reversed. As a workaround, use Single-Page Continuous display. – Brent Faust Aug 22 '15 at 20:52

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