Changes to appearance of repeat swatch and gradient (both with transparency applied) when .ai saved in PDF 1.3 compatibility

I need to send a complex vector print to a commercial printer who requires my .ai file to be saved as 1.3 PDF compatibility.  All the graphics display & print correctly bar two elements:
1. A gradient with transparency applied
2. A repeat pattern swatch with transparency applied
Both of these elements are layered between a solid colour background and a complex array of vector art.
The gradient displays as solid white when converted to 1.3 PDF.  The pattern swatch displays partly white, with some elements of the pattern repeat visible as a watermark.
1. I have tried to rasterise these elements within the a@rt, and while they both display correctly while in .ai format, as soon as I convert to PDF the appearance changes as above.
2. I have tried to apply the transparency to the paint buckets on the gradient slider instead of applying it to the shape with gradient fil
3. I've fiddled with the Transparency Flattening presets, Document Raster Effect Settings, and everything I can think of in the 'Save as PDF' dialogue box
4. I've tried to rasterise the full file with an even worse outcome (all colour information lost, appears only on grey scale with fewer elements visible)
Could this have something to do with spot colours or overprint?  Any help would be most appeciated!
I'm using:
Illustrator CC 18.1.1 (doc colour set to CMYK)
on a Macbook Pro OSX Yosemite Version 10.10.1
Apple Preview Version 8.0 (859)

Hi Mike,
Thanks for taking an interest! I tried rebuilding my gradient as suggested to see whether it would make a difference, but was still having issues.  Tried to save every which way with the save as PDF options in 1.3 profile.  Finally went back into the file to unpack each layer and see what I could adjust to save the appearance.
Found this fix in my swatches palette: for some reason the swatches I was working with had converted to "Book Colour", something I never use.  I changed the dropdown back to CMYK and changed the colours from spot to process, which fixed the file    Relief after hours of searching and late nights!
Thanks again!

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