Unfortunately, no change in behavior.
Exported to IDML
Opened IDML in 7.5.2 and resaved via "Save As" with a different file name.
Launched ID and opened file.
Exported to PDFx1a
Color box on page 4 still drops out.
Well, that's not terribly good news. You mentioned earlier that pages 2-4 export correctly, but 1-4 do not, so I wonder if the problem might be on page 1 rather than on page 4. What happens if you export just pages 1 and 4?
Everything is fine with pages 1, 4 exported but not with 1-4. I'm completely stumped. I filed a bug report offering to send the ID package if needed. I can't find any reason for this behavior. I've removed all transparency and overprints, even deleted page items one by one to see if it was some item causing it.
Really weird behavior.
Weird indeed. I think there is some sort of minor file corruption at play here, and unfortunately .idml isn't quite as good as .inx was at cleanup.
My next step would be to try moving the pages into a new document. Before actually moving the pages, though, rename Master Page A so it doesn't take control and load the styles from the existing doc if Basic Paragraph was used AT ALL, even as the basis for something. Like-named master pages and styles are controlled by the definitions inthe receving document when you move pages or paste content. Delete the original empty page from the ne file after moving the other pages in and try your export again.
If that doesn't work, make another new doc, same caveats about masters and styles, and COPY/Paste in place everything for the first 4 pages (since that seems to be an indicator and perhaps where the problem lies). If the new doc will export, I'd try moving the pages 5 and following into it. As an aside, copying threaded text frames is going to be a pain -- the threads will break and need to be re-established.
Iv'e discovered more..
I've removed all items I could.
Here's what the 4 pages currently look like.
Page 1 blue bar is solid pantone with an Indesign drop shadow effect applied to it.
Page 2 photo is a greyscale .psd with transparency.
Page 4 photo is a flat greyscale .psd, no transparency.
The light blue box on page 4 is 10% pantone and this is what's dropping out. All other page 4 items are always present on export. It's just that light blue box that's dropping.
If I export all 4 pages as they appear above to PDFx1a, there's no light blue box on page 4.
If I remove the drop shadow from the blue bar on page 1 and export all pages, the blue box on page 4 is present.
If I leave the drop shadow on page 1, and delete the photo on page 2, and export all pages, the blue box on page 4 is present.
If I delete page 3, everything exports as expected.
If I copy/paste page 4 items to page 3, everything exports as expected.
So... it would appear to be some sort of corruption or bug which requires the combination of drop shadow on page 1 + photo on page 2 = no blue box on page 4.
I'll chaulk it up to a "hinky" file. But I will be keeping a closer eye on exported PDFs for a while.