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It's almost certain to be considered cloaking by SEs if what's in their cache doesn't match what's available at the URL they indexed.
Does the ranking suffer if the same script is used even though it sends back unique pages?
Does it matter if .php is in the middle of the url or at the end, ie. will a search engine prefer domain.com/var1/var2/page.php over domain.com/index.php/var1/var2 (by prefer I mean 2 things, 1. any indexing problems? and 2. any ranking drawbacks?) Thanks.
However, you may have problems getting organic listings in Google using such a system. Google will only recognize so many parameters.
You might want to consider using Mod_Rewrite to translate regular URLs into the parameters... so that you could make links like this:
rewrite into this: