We have a client with 2 different MSM installs, and each install runs up to 35 different websites.
Years ago we set up a channel for each site that had about 30 custom entry fields that they used to control colors and images to style each site. We thought this was a great idea.
Right around the time we created site 20 or so, the database ran out of columns. Yes, it can happen and EE MSM will do it if your sites have a lot of custom entry fields. If I remember correctly, each field uses 3 columns and when you start duplicating sites you can actually run out of columns and once that happens all sorts of strange things may start happening.
You should search the forums here for listings of “
Database Error - Error Number: 1117” and also MSM issues for folks with large installs.
You may want to rule this out as a possible issue. If it is your issue, then you’ll need to rethink how you create your MSM sites to help keep the number of custom entry fields down.
Good luck to you with your solution.