I take it back. Problem is back and presenting differently. I just opened RStudio and opened a project. Opening the project opened three files: an Rmd file and two R files, in that order. When I mousewheel over the Rmd file, the Packages pane scrolls. Same thing when I then mousewheel over the first and second R tabs. But if I go back to the first R tab and mousewheel, the Console window scrolls.
Above is the typical behavior. I also noticed other behaviors, such as 1. the mouse wheel causing no scrolling at all in any window, 2. expected scrolling behavior where mouse wheel causes scrolling in the window the cursor is above, and 3. all uses of the scroll wheel in the editor cause the Packages pane to scroll up and down.