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I've created PDF files with Photoshop, then combined them to create a 16 page PDF. Photoshop's colour profile is set to SWOP (Newsprint), with Total Ink Limit set to 235%.
Depending on how I save the file (specifically with layers or not) seems to affect both the colour and the file size. Do layers have any effect on preflighting? Specifically, I'm trying to convert the file to X/1-a format.
Its best to pay attention to your layers from a printer stand point. When building a file for print layers do matter for the RIP and how it will process the CMYK. Text should be your top most layer. Photos next then Effects using transparencies. This is a really rough and general way to explain it. However, the way a RIP will process the PDF that you are mentioning is looking for the color separations and how to phrase the blinding of colors. If you have access to Adobe Acrobat Pro you can run these tests to see errors that are produced when converting to just about any PDF file and much more. Also look onto the features that will flatten your transparencies as well in this program. This is a good site for looking into Preflight - http://www.vigc.org/standard-preflight-profiles/.
I am not affiliated with this Company so please understand I am only sharing what I have found to be helpful.
The x/1-a standard doesn't allow for transparencies. So, in order to get a PDF to pass that preflight check, you should flatten your file (SAVE A COPY WITH LAYERS FIRST!). Then you could try remaking the PDF. Also, is the photoshop file you are trying to save RGB or CMYK? Make sure it's a CMYK document before trying to output the PDF to a print standard and you may get better results.
I would probably handle this a little differently though. If you have access to InDesign you can place the layered .psd files into a document and make a PDF with the x/1-a standard and it should be fine. InDesign will handle the transparency flattening for you and you should end up with a smaller PDF to boot! This method of placing your photoshop work into a document will also work with illustrator.
That said, there is probably a way to do all this right from Photoshop, I've just never output any file I've sent to a printer as a PDF from Photoshop. I'll be interested in seeing if someone has a different method for outputting a file directly from Photoshop to print PDF.
