Why are all my paths disappearing when I save some files as jpegs?

I have 2 identical PSD files. Both have 10 different paths that are identical for each file. When I flatten and save one file as a jpeg the paths stay in the file just fine as is usually the case. When I open the jpeg the paths are still there as they should be.
When I save the other file as a jpeg all the paths are there after I've saved the file and BEFORE I've closed the file. After closing and reopening the file the paths are all gone. If I save the same file as a tiff the paths all stay as usual.
I've never seen this happen in almost 20 years of using Photoshop.
Anybody have any ideas?
Thank you

I am NOT using "save jpeg for web" just to be clear.
If I were, then the other image wouldn't be keeping any of its paths either.
I am using "Jpeg" in the Save As dialogue box.
If I edit the jpeg that lost its paths after opening it and hit "Save" it gives me the compression options dialogue box. Other jpegs just "save" when I hit save, I've never had a jpeg give me that dialogue box before when hitting just "Save".
If, after opening the image that lost its paths, I paste a path into that image and hit "Save"(using one of the same original paths from the same original psd file), it gives me the compression dialogue box. If I complete the "Save" and reopen the image, voila, the path I pasted into it is still there, and, if I edit the image and hit "Save" it becomes normal again and saves without showing the compression options dialogue box.
Photoshop CS6 version 13.0.5
iMAC 27"
12 gigs of RAM 5 gigs free
800 gigs of free space on the system drive
Snow Leopard 10.6.8
Disk Permissions Repaired
There really is no reason for this to happen. There are no differences in the images except for the content of the image and the file names.
I have tried new file names and still the same result.
I have tried working from the Desktop and still the same result.
This is a serious bug.

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