To be safe, I would convert duotones to CMYK images in Photoshop: Image > Mode > CMYK Color.
Can you start a new document and then load one of the duotones known to be good in the working file and have it correct? If so, try one of the duotones known to be bad in the working document in the new file. Does it work?
If no to either suggestion, can you share one of the images known to be good and one known to be bad? ZIP 'em up and upload to dropbox and plop a link here. Or, to keep the file sizes down, you can quickly make a new set and provide those.
As well, the ID version and OS info would probably be helpful.
Take care, Mike