Good workflow to avoid white lines and discolored boxes with transperancy?

I'm somewhat new to Illustrator. I have designs in illustrator CS4 that contain objects with drop shadows that are on top of gradient backgrounds. When I save out the artwork as a PDF file I see random faint white lines and discolored boxes around the objects with the drop shadows. When I print proofs of the file on my HP3500 color laser printer I see the white lines and discolored boxes as well. I'm afraid the the lines will show up in production when I send off to the printer. Here's what I'm doing. Any suggestions would be appreciated.
(Document Raster Effects Settings: Resolution-High 300ppi/Background: Transperant/Options: preserve spot colors, add 12.7mm around object)
1. Save file as PDF from Illustrator CS4
2. PDF Settings
a. PDF Preset: PDF /xa:2001
b. Advanced Overprint and Transperancy flatener options: Preset-High Resolution
When viewed and printed from Adobe Acrobat 9 Pro there are white stiching lines that are visible.
Do I need to worry about these? Or will they go away when sent to a better printer?
Thanks for the help.

Try "Press Quality" Acrobat 5 compatable setting for "live" transparency. You can also try PDF/X-4 2008 which maintains live transparency and, in CS4, maintain Acrobat 5 compatability. PDF-X1 is a setting that "flattens" transparency which may limit your output options, depending on final output device. Double check your raster settings and make sure it is set for 300ppi/2400dpi and not 72ppi/300dpi. As suggested by Wade, your printer may not be a Postscript Level 3 output device with a RIP. So, the driver may not be screening the artwork properly and the stitching shows up in output. You may benefit from taking the file to a prepress shop and have them output a "contract" proof. If the stitching shows up in the contract proof, then the PDF setup may be the problem or the original file itself.

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