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Well if you can give us one reason why XOOPS should affect your other scripts (apart from the fact that you think it does) we are more than willing to investigate it.
I cannot see how it is possible, but there are things in PHP I don't know about and I am willing to learn. If you can suggest anything tangible, I'd be happy to check it out.
Nobody is calling you stupid, we just cannot see how it can be XOOPS' fault - and you are not giving us any arguments to make us change our minds.