Some questions (but will likely not be all of them!):
- Is this Mac-only? You didn't state your platform.
- did this work correctly in Acrobat X?
- does your document contain any overprinting or transparency?
- is the spot color used in a smooth shade, i.e., "gradation" or blend, if so is the other color also a spot color?
- are you using any RGB images or line-art, tagged or otherwise, in the document?
- Is it correct to assume that the spots display correctly when the Output Preview is closed?
FWIW, I have not seen any problems at all with displaying spot colors either in or outside of the Output Preview, but will try to replicate the problem. It is always possible that code was introduced late in the projcet that altered behavior, which we may have missed. There are also quite a few source applications that may handle the color differently before the file is a PDF, and it always is helpful to deconstruct the assembly of said project.
If I am unsuccessful, I may need to request the file in question, which we can do offline.
Could you please try something out, and that is to - besides reporting whether the spot colors are visible without the Output Preview - once when you are back in the Output Preview, to toggle the 'Simulate Overprinting' checkbox on and off, and see whether the spots reappear when the checkbox is deselected.
The next test is to find the panel in the Output Preview titled "Show", and to select "Spot Color" from the Show list and inspect whether the colors are all there.
Could you please report back in these cases, i.e.:
- spots view outside of OP
- spots toggle on/off when the 'Simulate Overprinting' checkbox is toggled
- whether all of the spots show in the SHOW/SPOT COLOR drop down menu inside of OP