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Old 06-20-2009, 02:39 PM  
MIS
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Join Date: Jan 2005
Posts: 127
From experience and knowing a decent bit about SEO, here's the problem, and it's probably 99.99% this problem only.

The same way google penalizes for duplicate content, they also have the same power to use on duplicate scripts, however with different algorithms. If wordpress did not have themes, plugins, and all that, they would have been forced to do it anyways. Your out of the box wordpress theme will have a hard time ranking in google.

To speed up the process of duplicate code/script penality, some one has to take that script and abuse google with it. The only way for google to stop this abuser, is to bomb all his sites that use the basis for his operation. His words and content could change, but his code will not change for the most part, which is the finger print google needs to stop the abuser. So everyone else was profiled as abuser too. However, I don't think this is the strong case here, this is merely a duplicate code penalty.
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