I recently had to re-install windows also install Rhino on other machine and I faced this (I consider a quite annoying) issue.
I import my settings and toolbars, that’s all good, but they are just dumped on the UI without keeping the arrangement. Also settings like Gumball/Ortho/Planar/Grid/ sub-object filter ON/OFF is not saved anywhere unless you save a 3dm file. I believe also the viewports has to be saved to a file in order to save the arrangment and configuration.
I think all this must be part of the config files and make this process much easier upon new-installs.