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I figured it out. It's because under Omnigraffle -> Page Setup, I had this document set to 55% and the page orientation setting is set to "Page Setup". If I either change the page to 100% or pick either Portrait or Landscape for the orientation, then the page size settings don't get messed up. Very strange!

I've also seen another bug where moving my cursor from the width to the height back and fourth would keep decreasing each field by roughly half (55%!)!