And when the order gets stored in your admin, what payment module does it show as being used to pay for the order? Admin->Customers->Orders, column 2.
I'll bet that it doesn't say PayPal at all for those orders.
In Admin->Modules->Payment, you see all the payment modules available to you. I suspect you've got some in there that you're not using, and instead of properly clicking "Remove" to prevent them being used, you merely set the "enabled" option to "false", thus allowing them to still activate under certain criteria.
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