While working on a Paypal test with a customer we noticed that the module appears to have an error which requires users to enter the IPN return url in their paypal account settings. This obviously means that it isn't possible to set up multiple stores using PrestaShop if you have a single paypal account.
The offending line (42) in paypal.tpl contains the form variable returnurl. The post variable returnurl doesn't exist in the Paypal documentation, but the value being passed is correct for the IPN url. This line should likely be notify_url instead.
We'll continue our testing to confirm that this solves the problem with IPN configuration for multiple stores using PrestaShop.
Update: Patched paypal.tpl file to address the above issue: Paypal.tpl updated