Maybe, for me at least, this wasn't actually a bug. I think I expected choosing "Delete downloaded packages after installation" would also clean out the packages in /var/cache/apt/archives already, but simply clicking the "Delete cached package files" button does this, and the "Delete downloaded packages after installation" option does keep the debs out of this folder after I install new packages, for 12.04 at least, marking this as invalid.
Maybe, for me at least, this wasn't actually a bug. I think I expected choosing "Delete downloaded packages after installation" would also clean out the packages in /var/cache/ apt/archives already, but simply clicking the "Delete cached package files" button does this, and the "Delete downloaded packages after installation" option does keep the debs out of this folder after I install new packages, for 12.04 at least, marking this as invalid.