I'm one of those people who logs all radio contacts, including those via a repeater. Thanks to the cool and upgraded features in cqrlog I can now set propagation type RPT (repeater) correctly on the Satellite tab for the contact.
But that will make the next upload to LoTW fail. tqsl will not accept the contact (which matches the LoTW rules: repeater contacts don't count). So tqsl ends with status code 9 "some QSOs suppressed" which means cqrlog will mark none of the contacts as uploaded and the problem continues.
I would suggest the best course of action is to filter contacts before submitting them to tqsl, I think Echolink, Internet-assisted, IRLP and Repeater should be filtered out.