Similar thing happened to me a few weeks ago. Called LH to book a RTW that included a trip to Lugano on an LX flight operated by Darwin Airlines. LH rate desk says it can't price the trip, as Darwin-operated flights are not included in RTW. (I had, of course, checked the list of ineligible LX flights, and the Darwin-operated Lugano flights were not on that list.)

Called LX instead, and the ticket was written with no problem.