We seem to be having the same problem, or somthing very similar. If I understand correctly, at checkout time the payflow module records the transaction id of the authorization in the paypal table. But if we then capture the payment, it doesn't seem to update the transaction action to the one in the capture transaction. So if we later attempt to refund from this charge, the only transaction showing in the order record is the original transaction id of the authorization. The payflow module doesn't seem to keep any paypal_status_history records to keep the various transaction ids for each charge, unless I'm missing something. The only recourse is to log into PayPal Manager and find the transaction id of the capture, by which time we might as well do all the refunding or whatever processing there. It makes the buttons on the order edit page pretty useless, after the initial capture has been done.

The module also seems to omit the billing name/address from the authorization transaction. So if we look in PayPal Manager to capture the payment, one of the security checks is to compare the bill info vs. ship info. But with the billing info missing, we have to look back at the Zen Cart order to see if they are the same.

We have similar loss of functionality in paypalwpp. We used to be able to refund partial amounts, but can now only refund the total amount.

Do we have up-to-date modules? What might be a recommended solution? Have I posted enough info below to define the problem?

Let's see if I can give the relevant background info:
Zen Cart 1.3.8a
payflow-1.3.8 payment module downloaded from a forum attachment to a post by DrByte in May, 2008, set to Auth Only.
Also using paypalwpp module bundled in ZC 1.3.8a, set to use PayPal API

Probably not relevant, but also using googlecheckout payment module ver. 1.4.7

If these problems have been addressed before, I would love it someone could link me to the relevant posts. I couldn't seem to find what I needed with the forum Search.