Nobody really knows what explorer does or why outside of Microsoft. I haven't seen explorer refresh as soon as it's openend, but the 1-2 second delay is especially annoying when you want to rename two or three files in a row. Somehow I think there was a halfway rational explanation for this, but I don't remember it atm. It has nothing to do with hardware or CPU load though.

As for setting explorer as shell from a popup: See the documentation for SetShell if you used Omar's installer. (specifically the sections "COMMAND LINE OPERATION" and "MISC")