I have exactly the same problem and I find it is specifically when raster effects like drop shadow or feather are used.
I think its important to not that these lines don’t appear on the final printed material. That doesn’t help me when I’m exporting for screen…
I tend to print to pdf instead of saving to pdf as this keeps the file size down somewhat. The preserve editing capabilties isn’t available in the print dialogue as far as I know. Expoting to jpeg, then re-exporting to pdf from photoshop is simply not a very practical option in my workflow.
Any other tips would be most appreciated.