I'm only your fellow user - not anyone from Microsoft. I'm sure that someone from the Photosynth team will reply to you after the weekend.
Would you mind uploading these images to a public OneDrive folder?
I'm not certain where you're seeing the "3 omitted" message. Is it on
1) the 'upload completed' page or are you seeing it
2) when you actually view the synth and click the Information icon in the lower left corner of the viewer?
If it is the second option, then '3 omitted' is only telling you that Photosynth was not able to match 3 of the photos to the others.
I can't say that I've ever received a message that the reason is that the images are not formatted JPGs, though.
I don't know the origin of these three images in particular but if they were ever not formatted as JPGs, I trust that you know that simply renaming the file extension on the filename will not convert them to JPG formatting.