I am having the same problem, and I can’t find any guidance on this in the archives.
WordPress version: 3.4 (issue persists from last version)
WordPress SEO version: 1.2 (ditto)
Theme: Woothemes Swatch 1.4.8 with “Use 3rd Party Plugin Data” selected in SEO settings
I did this: deselected the radio button for “Use Meta Keywords Tag?” I had turned on for testing
I expected the plugin to do this: be deactivated
Instead it did this: button remains checked after save + refresh
