The MMD3 skin that was originally developed by Sven Kistner for Winamp3 v.10 and that is still offered as a download from
Winamp.com has been known to not work properly in / have issues with Winamp 5.05. That might have something to do with your problem. Try the unofficial Winamp 5 updated version instead, from the
MMD3-for-5 update thread. Download the ZIP file from the link in
this post, and read the Readme text file in the ZIP file, to determine which MMD3 skin you prefer to use (2 to choose from, each one handling visualizations differently).
You also said that you have 2.91 still installed. I'd uninstall it if I were you. You should only be using
Winamp 5.05 because it fixes many
bugs and security issues, including this
major security issue that still exists in older Winamp releases (also mentioned in more detail
here).