Milan, I've got the same problem here. LoTW gave me two new band/countries for the DXCC Challenge not confirmed by paper cards. The "Reports / DXCC / Listing / Select ALL / ALL modes, ALL" doesn't show a "C" for them, although the "Upl Cnf" flag in the QSO window is "Y".
It would be nice to have the LoTW confirmations show up in the Listings as well. Hopefully Paul can add this to the next release. Cliff K0CA
