I was working on setting up a clone of my store's setup (long story, basically setting up for a foreign language affiliate) and I did this by copying everything and then scrubbing the DB clean of the customer, order and product data.
During this, I noticed something that might possibly aid in the solving of the Paypal IPN issue.
I noticed before, and I think that I mentioned it, that when the transaction type is "unique" that the Rewards Points aren't assigned. and that when the transaction type is "web_accept" that the points are awarded properly.
Well, when cleaning my DB, I noticed a few other things as well regarding Paypal (I use only Paypal IPN for Paypal -- the RP mod works wonderfully for our CC processor)
When the transaction type is "web_accept", the following is true:
module_name = "paypal 1.3.8a"
module_mode = "PDT"
When the transaction type is "unique", the following is true:
module_name = "paypal (ipn-handler)"
module_mode = "IPN"
I am hoping that this info helps in some manner.