After that, when looking at the search results and viewing the preview thumbnail, I saw that Google had immediately indexed the code changes and the new logo, but NOT the CSS changes from two days before.
Hi agent_x welcome to the forums,
why google would fetch the css for its index? It fetches the html part that has the references to the side scripts like css, js etc. And so when you view the content with your browser the later pulls-in the css from the site or any other resource that is listed in html head section.
It's good practice to setup the html so the fully qualified paths to the various resources is used. I am saying this in case your html base tag or some path reference is not resolved correctly and viewing the google's cache or preview etc, doesn't render parts of the page (after the recent mods you made)