I'm wondering how it was possible to do a 16:9 encode without the stream being correctly flagged. I don't really know TMPGEnc, but 16:9 vs. 4:3 is usually simple output option when you specify video quality settings - in addition to any resizing that may be necessary, this sets the flag accordingly.

How was the original transfer formatted - I assume it was actually recorded to video/file via a 16:9 camcorder? If you were using an automatic setting or preset, I suppose the footage might have been misinterpreted as 4:3 - the optically squeezed picture information would still be there, but the resultant file would be tagged as 4:3.