I narrowed it down to two items, it was permissions - 644 made emails bounce and not import into WHMCS, changing it to 755 fixed the problem - the path in config.php in the Crons folder. The path was ../ but that failed, with permissions set to either 644 or 755.
The path has to be absolute it appears, so upon upgrade, somehow config.php in the Crons folder has to know where WHMCS is installed, otherwise we'll be having these chats regularly : ) The permissions thing is puzzling, but at least there is a workaround.
Anyway, I'll be paying closer attention upon the next upgrade : )
Thanks for all your help.