To me this looks like a bug in Mono System.Configuration because it should know about the asp tag prefix and its mapping to System.Web.UI.
For our own custom server controls we have to tell it about the tag prefixes in Web.config under the pages > controls section like this:
<add tagPrefix="portal" namespace="mojoPortal.Web.UI" assembly="mojoPortal.Web" />
so you may be able to help Mono past this bug by putting something like this in the same section of Web.config:
<add tagPrefix="asp" namespace="System.Web.UI" assembly="System.Web" />
which may help it know where to load the type for the controls from.
Just a theory but I would try it.
Hope it helps,
Joe