I’ve hit this problem too, where I cannot add any more sites to the WP install, which has at one time been an MU, had multi-site plugins, and other jiggery pokery to make it work. The site has been moved from server to server and although it now continues to run the existing sites (all using different domain names pointing to the same IP as the root site), I can’t add any new sites to it without manually creating the database tables. It’s not an .htaccess problem, I believe, but rather a consequence of using a very old baseline (vintage 2004).
The solution is either to create the tables for the new site ID manually, or run a new instance of WP. The latter feels less dirty as a solution.
Hope that helps.
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