As per my above comment...
Under the "action" column in paypal.com, for the record of type: Payment, rather than type: Authorization, I only see "print shipping label" as an action. I'm not sure if that column is an indication of what parts would be exposed in the API that zen-cart uses. Under the record for type:Authorization there are no available actions.
I also checked out a transaction that I had not captured, and compared the actions available for this transaction in paypal.com. Under the "actions" column they offer "capture" and "ReAuth", but upon clicking "Details", I also have the "Void" option.
In the zen-cart comments for the authorization and fund collection there is a Transaction ID and a Trans ID, and I thought it was strange that the two were different although the Trans. ID (notice the punctuation after "Trans") matches "Transaction ID" instead of Trans ID.
Upon looking in Paypal.com, I noticed that the Transaction ID: xxxx(see below for the zen-cart comments) for the authorization, it matches the authorization transaction ID in paypal.com, which would seem to indicate the correct transaction is being accessed. The payment received part in Paypal.com also matches the zen-cart funds collected comment Trans.ID.
So I don't think the ID's could have something to do with the incorrect rejection of payment refund...but here's what they look like (with important info stripped out):
Here are the comments:
First:
Transaction ID: xxxx
Payment Type: Credit Card (WPP)
Timestamp: 2008-12-02T00:22:33Z
Payment Status: Authorization
AVS Code: blah
CVV2 Code: blah
Amount: 0.04 USD
Second:
FUNDS COLLECTED. Trans ID: yyyy
Amount: 0.04 USD
Time: 2008-12-15T20:55:44Z
Receipt ID: zz-zz