I might found a solution.
Like I said, I created and exported the tour with PanoTour. After that I selected all files in the folder and dragged it into the krpano Updater. I believe that the updater is not doin' so well. After I replaced the krpano.swf, swfkrpano.js and krpanoiphone.js it worked.
I have to add: after exporting from PT my swf was "virtualtour.swf" and I replaced and renamed the virtualtour.swf with the one from the krpano 1.16.3. They also differ in file size, 98KB PT and 96KB krpano. I also believe that the updater is not correctly recognising the main swf because there was no backup at all, if the main swf has a different filename.
It could be an explanation.