Making a PDF with an image that has both spot colour channel and alpha channel

Hi I have a logo that was supplied to us as a PSD it has a transparent background, it also has a pantone colour channel. I have made a alpha channel from the transparent background as well.
The graphic looks fine in InDesign (alpha channel selected in the import options), ie the background is transparent.
But when we try to make a Hi Res PDF the result is that the graphic is on a solid white background.
If I go back to the PSD and merge the spot channel with so that it is just CMYK and try again the PDF is fine, but we obviously loose the spot colour.
How do you make a PDF with a transparent PSD that has a spot colour?

You know that annoying response from support staff? "We cannot replicate your issue". Well....
I created a PSD in CS5, with a bunch of process stuff, then loaded a spot color channel and painted in some pawprints using Pantone 172C:
Saved this as a PSD file, default settings (maximize compatibility on, but it doesn't make any difference in this situation).
Created a new InDesign document in CS5, added a gradient and some text, then placed the PSD. ID understands the PSD has an inbuilt background so there's no need to bother with a dedicated alpha mask:
Exported from ID using the High Quality Print option (PDF/1.4, which keeps the live transparency):
Re-exported to PDF/X-1a (based on PDF/1.3 which flattens transparency) - looks exactly the same. In all cases the spot channel is intact and the see-through regions of the PSD are maintained.

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Making a PDF with an image that has both spot colour channel and alpha channel

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