Vector elements are randomly disappearing when saving a PDF file

I wondered if anyone could help us with this.
We make PDF files from Illustrator all the time to send to our clients for approval. We've found that occasionally random elements of the document will not be embedded within the PDF file.
There seems to be no consistency with this, an outlined word on one side of the artwork will vanish one time, it'll be fine for the next 10 iterations, but then a totally different element will drop off on a different part of the document the 11th time I PDF it.
All seems to be fine within the Illustrator document, layer/item visibilty is ok, overprint settings are correct etc.
I have imported an affected PDF file back into illustrator to see if the element was gone or just not appearing, and they're completely absent from the file.
This seems to be particularly happening with items that are coloured with spot colours or white elements sitting on top of spot colours, but this is not certain.
This problem is very concerning for us as we deal with quite large packaging files and it comes that we can't trust the files that we're sending to our clients to be accurately representational of the actual documents. We can't be spending the time to be having to check every individual element on a PDF file every time we make the slightest amend to a file.
Thanks in advance for any help you guys and girls can give.

What pdf preset are you using (eg: smallest file size). Are you mac or PC, the pc works pretty good printing to the pdf writer. During your 10 iterations, are you making any changes to the files, or are you saving the same file over and over and the result is different each time. What happens if you go to another computer and try to make a pdf form the same file?
You large sized files, scale a troublesome one down to fit on smaller paper size (eg: letter or tabloid) and make a pdf. Are your PDFs taking a long time to make? Try cleaning up nonused spot colors, and making them global.
I make lots of PDfs and can remember 2 cases where things were acting funny, but resolved this
Embedding a placed 1 bit tiff that was being colorized to a spot color - the pdf span forever and never made itself prior to embedding
Creating outlines on a complex appearance stacked logo, where the corners were missing triangles.

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