Problems converting from .ai to .eps/.pdf

I recently designed a logo for a client that included both a gradient and transparency.
I flattened the transparency, expanded the strokes and embedded the text before saving a copy of it in .eps and another in .pdf (PDF/x-1a:2003)
When I opened both files in Preview, I found these two problems:
I didn't have this problem when I saved the file in other formats (.jpg, .png)
What caused this and how can I fix it?
Also, while I'm here, is PDF/x-1a:2003 preset optimized specifically for printing?
Thank You!

JPG and PNG are mostly for web work and essentially rasterize the art--the problems you're seeing are the result of stitching (a process that takes place when transparency is flattened)--if you are prepping files for 'print house'-- DON'T FLATTEN transparency or expand strokes, embed text. or save as .eps or PDF/x-1a--instead--just save as .ai and .pdf (use the 'illustrator default' PDF setting) that will allow the print house to use their RIP to process the file(s)--unless of course, the print house has 'specific' settings they want for PDFs--in which case, call and ask what setting they prefer (note: the illustrator default PDF setting will generate a larger file, but that's why there is so much portable media available-ie-CDs, DVDs, thumb drives, and a variety of free FTP sites to send files to printers).

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