I've heard of a similar issue once before, but I have no idea what could cause it aside from some kind of a more general MySQL server problem. Or maybe some arcane race condition that makes WP create new wp_sitemeta entries instead of updating the existing ones... AME doesn't really do anything special with the database in general or wp_sitemeta in particular. It doesn't even run any direct SQL queries. It just uses standard WordPress APIs to load/store the menu configuration.
Some thoughts:
- You mentioned SQL errors. What were they? How did you determine that they are related to AME Pro?
- Does the number of
ws_menu_editor_proentries match the number of sites where you activated this plugin? If you activate it individually on each site (as opposed to, say, installing it inmu-plugins), it will create one DB entry per site to store the menu configuration. - On a related note, were there multiple entries per site, or perhaps all of the entries were for the same site?
Side note: This support forum is mostly intended for free plugins. Please use this contact form for Pro-version-related support requests in the future.