Which method are you using to produce a pdfx file?
Personally i use the first one,never having a problem.
In my previous job we saved ps's -from inDesign- and then distilled them,but i can't quite understand why should anyone still use the distiller.
We always try to use export to PDF. It's faster and can preserve transparency in addition to more robust handling of color management.
If your RIP is up-to-date there is really no downside in comparison to PS+Distiller. And even with our older RIP we always exported to PDF. PS+Distiller is a thing of the past, if your application can directly export to PDF.