Photoshop CS4 - Layers Missing in PDF Export

Hi there,
I'm working on a leaflet design for a client in Photoshop CS4 and am having a real issue with the PDF export. There are three layer groups all containing the same graphics, but when I export these to PDF - whether compressed or uncompressed and I've tried Reader 5 - 8 compatibility and with varying settings the layers do not appear in the PDF.
They are visible as plain as day in Photoshop, but don't appear at all in the PDF.
Any help would be gratefully appreciated,
Many thanks,
Martin Oxby
mOxby Design
Custom Web Design

Thanks for your answer :-) I will try the gradually merging option first. I did flatten it but lost a LOT of quality in the PDF, which is not great when this has to go to the printer's.
My image doesn't have clipping paths (probably hard to believe) but does have an epic number of layers. Here are the offending layers - nothing complex at all. The layers that don't appear, simply are the three squares which are in the 'Logo Squares' layer group.
If this enlightens you at all please let me know and I'll get back to you again. Thanks for posting!

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