The full error is
The base class includes the field \'ScriptManager1\', but its type (System.Web.UI.ScriptManager) is not compatible with the type of
We had a very similar problem. The development platform worked fine but once the site was deployed to the testing site it broke with the same message as the original poster above. We had subdirectories under our controls directory to group user controls together. The problem appeared to be a control in the subdirectory trying to use a control in the directory above it. Our first fix was to clone the toplevel control to the subdirectory. We then hit on the idea of creating a parallel sibling subdirectory and parking the control there. That fixed the problem without having to resort to (a) flattening our controls directory structure or (b) clone the same control in various subdirectories.
So our solution is to never refer to a control in a parent directory from a user control in a subdirectory.
I hope this helps out.