Yes, I already tried "don't open any listers" under "startup" in the configuration dialog as well as check the radio button to "shut down Opus after the last directory closes." I notice, also, that under "Explorer Replacement" Opus doesn't exclude all of the folders I have designated as excludable. Is there some Opus program cache I need to clear to make my option selections stick?
If you turn off Explorer Replacement and reboot, do you get Explorer windows opening instead of Opus ones, for the same folders?
If so, it isn't Opus itself that is opening the windows; something else is launching folders on reboot and they will open in whatever the default file manager is. This is often caused by things putting folder shortcuts in the Start Menu, Startup folder, or by things which add "run on startup" settings to the registry but do not quote their paths properly, so that a directory (with a space in its name) gets run instead of a program inside of it.
Your instructions solved most of the issue. Now the only Lister opened on reboot is the desktop folder for some strange reason.
Does it still open if you turn off Preferences / Launching Opus / Startup / Launch Directory Opus automatically on system startup?
If not, does it open again when you turn it back on?
(If that solves it, the arguments in the startup shortcut may have been incorrect or outdated. OTOH, if Opus still launches during restart when the option is off entirely then something else must be launching it; check with a tool like AutoRuns.)