Atlantis III may be the same game as Beyond Atlantis II, but it installs in a different game folder and the patches for the two versions may be different. You can find the old patch for Beyond Atlantis II on the Internet archive. There is a link for the Beyond Atlantis II patch on the web archive version of Dreamcatcher/Adventure Company's help page ***HERE***
(scroll all the way to the bottom of the page to find the link).
Note this patch was from 2002 and may not help with other issues that may happen with modern computers. For example if there is a problem at the same location that happens with widescreen monitors, the patch is unlikely to help.