Sounds like you have a plugin running maybe WebNative by Xinet? Use PDF/X-4 or avoid transparency. The lines are from flattening transparency which is required with x-1a.
Ummmmm... Last I checked, PDF/X-1a was Acrobat 4(PDF 1.3), so it's never going to pass that filter (aside from the "Standards Compliance must be None" which probably rules out PDF/X-4, as well).
Is this WebNative check something from the printer, or something local on your machine? If it's on your system you ought to be able to disable it in Extensions Manager and then you can probably use any settings you like.
it seems like the Machine im working on has a plugin using WebNative tool?. Unfortunately I have no admin rights to the extensions so I cant seem to turn off this feature. Is PDF/X-1a 2001(PDF 1.3) a standard Printer option these days? I suppose most printers supply their own pdf and flatterning settings.
I switched the PDF/X-1a 2001 to PDF1.4 instead of 1.3 and changed the Flatterner preset to 2540ppi and it bypassed this error. Also the lines dissapeared (Acrobat still highlighted the flatterning so I turned the pref off, rasterised the pdf in PS and the lines were gone.)
it seems to only pop up when using the PDF settings.
Look at this thread (from #20 on) for pros and cons of x-4 and x-1a standards. Sounds like you need to find away to disable the plugin.
I switched the PDF/X-1a 2001 to PDF1.4 instead
The lines went away because you are no longer flattening (not because you changed the flattener preset). You should also see that the standard switched to None.