Site URL missing http and user_tables missing from db

Good day,

Over the last few days we have had a number of problems reported that all have similar issues but we have not been able to figure out the issue yet.

We are running a multi-network (4 different networks i.e. http://my.wp.com, http://new.my.wp.com, http://123.my.wp.com and http://last.my.wp.com), multi-site (about 600 sites spread over the networks) system. We have had users create sites, build them, then they disappear. the symptoms of the problem are as follows:
1. if we go to the admin panel on that network and look for the site and look at the Site URL it will be missing the http. instead of having http://my.wp.com/xyz it will have ://my.wp.com/xyz.
2. If we go to the database and look up the user and the site we can find entries in the wp_users table and the wp_blogs table defining where the site should be.
3. If you use the blog_id and try to locate the db tables for that users blog, they will be missing i.e if the blog id is 108, tables wp_108* are missing from the db).

There are two methods to fix this that I’ve come up with, one – delete site and let them recreate, or restore the tables from backups. Although I can do those, I’ve had this happen too many times now for this to be a “coincidence”. Trying to figure out what is causing it and how to prevent it.

Any thoughts??

Thanks
DAve