PDF-X1A is just one of many pdf standards for printing. You still have to specify the correct output profile when exporting as a pdf. It's almost always best to convert all you RGB files to the proper CMYK in Photoshop before placing them in InDesign. I'm assuming you are using InDesign, right?
What is the profile that your printer specifies? What is their spec'd total ink? What paper are you printing on?
The biggest rookie mistake most people make when exporting to pdf, well the two biggest mistakes are leaving the default settings. You want to go in and make sure that you are NOT using jpeg compression on your CMYK tiffs - and you should be using tiffs. Use zip compression. The second thing is that the default setting when saving a pdf -x1a is for Acrobat to automatically convert your file to whatever profile happens to be loaded in Acrobat. You absolutely need to set that to Do Not Convert colors. It's as if the people who wrote the output module for Acrobat knew nothing about printing at all. Although it sounds like you printer might not know too much either, but that's no surprise.
