Strange layers issue when printing

Hi Guys,
I am having a strange issue which is probably easy to fix however I am not a heavy adobe user and dont know where to start.
This is the rough process to explain my point but a summary is - when printing PDF files they do not appear as they do on screen.
A picture/document is created in Adobe Illustrator, an outline PDF is then created and saved
I can open the outline PDF successfully, in newer versions of PDF Reader (v8+) the PDF displays on screen correctly. In older versions the PDF is missing lines or various things.
If I print this PDF all these lines etc still missing. I know this sounds vague but I will try and explain.
An example is this - the document is a black box with a silver smaller box on top in the centre. On the screen it shows correctly. When I print, the black box is printed with no silver box.
I have just discovered that the silver box is actually printed however its printed in the background so I think its got to do with layers? If I make the black box to be white, and then print I can see my silver box, so its clear it has been printed in the wrong order.
Oh another thing I have found is the default format for saving PDF files is v1.5 if I choose an older version, the layers are printed correctly
I have both Adobe reader installed on Mac's and PC and the issue happens on both
Surely all the printers I have can't be all in-compatible
Printers:
Kyocera KM-4050
Kyocera FSC5200
Canon MX850
Lanier MP2500
Lanier MP2800

This is not a scanning resolution factor and I have been scanning this way for years. These scans are not photos but documents. This problem just started.  And as I said before, the problem also occurs when doing a save as from Illustrator, as well as supplied files from clients, so the scanning process has nothing to do with it. I just can't get them to print right.

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