Pdf stitch lines, now visible in channels

Hello.
Having recently updated to Creative Cloud, I've notice that the pdf stitch lines scenario has changed somewhat.
I am aware that, for many years now, when exporting a pdf (Acrobat 4 PDF 1.3) any transparency layers within the artwork result in very thin white lines being visible on the file.
I had sent thousands of artwork out to press in that way, and was confident that the lines would not print.
One of the ways I would put clients minds at ease though would be to rasterize the file into Photoshop, save as a jpg and hey~presto, said lines are all gone.
Now, (since CC update) if I rasterise a pdf, the lines do show! They're there in the channels, ok albeit very faintly, but they are there.
If I flatten, and save as a jpg, they're visible.
Has anyone else noticed this since the CC update? I'm still new to it, so I'm sure some of you have.
Just hoping someone can put my mind at ease, and say they're ok and still will not print.
Below is the cyan channel, rasetrized in Photoshop
Iam using InDesign CC, on a mac 10.9.1

No, I don't think so. There is a export to pdf section. Which I use most of the time.
I also tried to export a postcript file, and then the pdf version 1.3 can be selected in Distiller after. Unfortunatley this produces the same result.
Since asking this question on here, I have posed the same query to a few of the printers that I use. They are quite sure the lines won't print when they output from the pdf.
The thing is I can't print from a pdf properly on our desktop printer here, hence why I rasterize to output proofs. I'm thinking this is where my problem stems from, something to do with how Photoshop recognizes the flattened pdf file.
Thanks for your replies Phillip.

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