Ok I searched through my old notes to see if I had something jotted down and ...

Ok I searched through my old notes to see if I had something jotted down and I found few things,

1. Transactions working on Paypal end, but IPNs not working
2. IPN URL needs to be added in Paypal merchant, after that IPN should be received, can be checked by adding a watchdog in uc_paypal IPN callback
3. The code for checking invoice ID in IPN needs a OR with rp_invoice_id
4. The invoice updating, order_comment_save, reporting, etc other housekeeping needs to be checked for end to end working.
5. The problem might be related to UC & UC- Paypal's IPN callback
6. A hook for IPN handling might be good, invoked by uc_paypal
7. uc_recurring can use this hook to do housekeeping etc on its end
8. Not sure if we need to expose entire IPN via hook, some important stuff should be fine, security and other modules interference should be considered.

Hope this helps,

Cheers