Sorry: My Mistake -- I was looking at the wrong entry...
Here is the error line for the sale that did not get tracked:
<--snip-->
[03/01/2010 5:51 AM] - SUCCESS :Updating Products, Customers, Coupons, Sales Database Tables with Sales Data.
[03/01/2010 5:51 AM] - SUCCESS :Products, Customers, Coupons, Sales Database Tables Updated.
[03/01/2010 6:58 AM] - SUCCESS :Paypal Class Initiated by 66.211.170.66
[03/01/2010 6:58 AM] - SUCCESS :Post string : mc_gross=-
<--snip-->
The log stops at "Products, Customers, Coupons, Sales Database Tables" and then re-starts an hour later when I processed the refund (since it was a test, and the sale had not shown up in the system).
Sales since then seem to be checking in with the Affiliate plug in no problem:
[03/01/2010 11:09 PM] - SUCCESS :Products, Customers, Coupons, Sales Database Tables Updated.
[03/01/2010 11:10 PM] - SUCCESS :MailChimp signup operation performed. Return value is: 1
[03/01/2010 11:10 PM] - SUCCESS :Updating Affiliate Database Table with Sales Data if Using the WP Affiliate Platform Plugin.
[03/01/2010 11:10 PM] - SUCCESS :WP Affiliate Platform is installed, registering sale...
[03/01/2010 11:10 PM] - SUCCESS :No Referrer Found. This is not an affiliate sale
Thanks