Actually I have the same problem, already in two cases.
I booked LH from Korea to Germany through my TA in Germany. Itīs a business class flight and it shows perfectly well on Checkmytrip. But on the LH website it keeps saying "booking could not be found".
Same thing with my wife- another LH ticket, shows up on CMT, but could not be found on the LH website.
Any suggestions? Tried with First names etc but no success...