IIRC, if even the robots.txt on a site gets changed, it's applied retroactively to the wayback machine. So older versions won't get shown.

I'm quite concerned about this for some domains I no longer control.

They show an IIS "404" page for part of one of my sites. It was always served under linux / apache. They have the rest of the site still; i dunno why they wouldn't archive the "Annotated Constitution"