Spot colors now missing in PDF!

Issue: spot color channel not showing up in Photoshop generated PDFs. Worked previously, this just started last week.
Workflow: receive PDF ads from client via email. Open file, usually Jpg, Tiff or PDF, in photoshop CS4. save as PSD, with new name, grayscale, 300 dpi for newspaper printing.
some ads  get spot/PMS color added.  add spot channel. move art from grayscale layer to spot color layer. save file as PSD with spot colors. (for import to InDesign.) Photoshop file looks fine on screen.
for Client proof, Save As "ad proof", turn OFF photoshop editing, so client does not change ad. Turn ON "as a copy", "spot color" and "view PDF".
It worked fine for the past year, now, NOT. The PMS spot channel is not showing on the photoshop generated PDF, If I import the psd file into Indesign, and generate the PDF 1x version, same thing.
Spent 7 hours on phone with tech support, they did not have a clue as to why or what was going on. I have uninstalled, deleted everything Adobe, and spent 7 hours reinstalling CS4.
Newly installed Photoshop not working, same issue. Print to PDF using PDF 9.0 "printer"  not working.
HELP!

I just had a very similar problem using CS5 Master Suite.
I had a CMYK job (a business card) that needed converting into a spot colour job.
There was a logo in CMYK that was red, blue and black, so I created 3 new channels in Photoshop and separated the colours into each specific channel. I saved the logo as a Tiff file and imported the logo file into Indesign. On-screen it looked fine (black, red, blue) and I could see the new spot colours had imported into the swatches correctly. However, when I exported the Indesign file as a PDF, one of the spot colours was missing (the red one).
So I changed the logo file (Tiff) into a Photoshop file hoping it would fix the bug, but no such luck.
Out of interest, I duplicated the Red channel and repeated my procedure, this time when I made the PDF the blue channel that was there previously disappeared!!!
When I checked the forum and heard that the poor person spent 7 hours with tech support, I thought bugger that, I just saved each channel as a separate Tiff file, dropped the black file onto the logo so that it was in place, then did a Step&Repeat (ie copied a duplicate of the logo ontop of itself), then dropped the new Tiff file on top of that and changed its colour to Red in the Swatches, and did the same with the blue file.
Now I have a PDF file that shows all the different spot colours and I can go home on time tonight.
I could do all this stuff on CS1. The only 'improvements' I have found in CS5 so far is that my beloved 'Variations' option in Photoshop has now disappeared because they couldn't be bothered to create this feature in 64 bit.

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