PDF file doesn't match Illustrator file...? Please help

hi all,
We have had a very unusual situation that need your help to find out.
Description: The artwork is an outlined Illustrator file is absolutely correct as the client wanted it be. Before sending it for production, we make an PDF file of that approved artwork. Well... The pdf DID NOT match the artwork and IT SHOULD MATCH.
Some of the vector background drop out/missing, some of the transparency of vector artwork went to 100% or wrong transparency...
Software used: Adobe Illustrator CS3 version 13.0.2 / Adobe Acrobat 8 Professional version 8.1.3
Hardware: MacPro 4Gb Ram, OS X10.5.6
thanks a lot for you help,

Thanks Laura,
This incident happened only once. I re-made another PDF using the same method and it was fine. I tried many time but I can't replicate the error/problem. The areas where was dropped out in the PDF is a solid color oval with 80% transparency, the other area is a gradient color with 100% transparency. There are similar areas like those in the document but strange enough they are not affected....
The PDF is exactly as expected on the Overprint Preview (using the very same outlined AI file, there is NO spot colors).

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