I stumbled upon a jpeg which is a scan from a slide (from 1992) and saw that iMatch displayed it rotated by 180°.
I checked in Photoshop and Bridge and it showed the same rotation there, so it really was wrongly rotated (probably during the scanning).
I tried to rotate it in iMatch via the lossless jpeg rotation function in the right-click menus.
Only that single file was selected and yet, I got an error saying that at least one file in my selection wasn't a jpeg and couldn't be rotated ...
So I tried to rotate it in Bridge and there it worked fine and iMatch soon automatically picked up the change and now it displays in the correct orientation.
Attached the debug log from that session where I reproduced the issue and the report from the Metadata Analyst. There are errors, but none with an orientation tag and it is definitely a jpeg file.
I would need to look at the file itself (before you modified it in Bridge).