Are you seeing any clues in the mojoPortal log under Administration > System Log?
Note that Site Membership Pro does not currently support recurring payments, so if there is something configured in your paypal account to do something with recurring payments Site Membership Pro is not currently built to handle that if PayPal is sending some kind of different information back. It currnetly handles only single payments and it can send reminders to renew membership.
Basically the way the PDT and IPN handler works is that the order is serialized into the mp_PayPalLog table and the log guid is passed to PayPal. Then when paypal posts back it includes the log guid so we can lookup the log row which also has data about which provider (ie feature) should process the transaction and then it loads that provider and passes in the data. The PDT Handler must also be defined in a file in the /Setup/ProviderConfig/paypalpdthandlers folder, there should be a file in ther corresponding to Site Membership Pro, that file is what it uses to load the provider listed in the log table.