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PHP is not "script" per se, but a server side thing. Java runs on the end user's computer (ie: when I go to that webpage, a java program is run on my computer). Because of the potential for security issues with this arrangement, and the number of ways that this has been used to redirect or otherwise defraud link sites, they are basically blocked.
You can do affiliate tracking with PHP that would be invisible and not requrie scripts to run on end users computers - and be much more accurate. Many people do not permit java to run on their computers, so they would not track.
Alex
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