I have the same issue, using Illustrator CS3 then creatind a PDF /X 1 a:2001, (spec wanted by my printer). Lines are there even in the proof of printing (on screen) they sent back. We've tried to print this proof document and lines are GONE. Let's see now when they print the magazine! I'll keep you posted.
Looks like this is an old post, but if you change the Acrobat version to anything above 4 when exporting from Indesign or Illustrator, the lines go away. I still don't know why the lines appear, but this is what I do for proofing to clients. The only downside is that it makes your document no longer 100% X1A compliant. But since the white lines don't seem to show up on a commercial press, it should only be an issue with proofing (having to explain the lines to clients).
3. Distillation (PDF/X-1a;2001)
A couple years ago, I was told by an Adobe employee, in a seminar that PDF/X-1a;2001 doesn't support transparency. Use a more recent set-up; anything that has the year 2004 or above, in it, should work.