Due to a macOS bug, sometimes certain windows will animate when the resize. This causes the window to not be resized to the proper location. The only way to workaround this bug is to introduce delays in the size/positioning changes sent to a window. This early alpha release includes the logic to add in these delays, but you must configure them with the following Terminal command:
defaults write com.knollsoft.Rectangle animationDelay -int 300
300 is the number of milliseconds to wait between every size and position call made to each window, and can be adjusted as seen fit. It's arbitrarily a number that worked OK for me.
Note that there are existing issues here - repeated shortcut execution does not perform 2/3 and 1/3 sizes (if configured), and 300 ms might be on the low end of what is needed to allow the window to fully resize from/to certain sizes/positions.