A couple findings:

I have it set to 3 IP address, unlimited downloads and no expiration. When adding the File Download feature to one of our products, checking "Retroactively purchase" in the process, the associated files did not show up under My Account. They only appeared after I went into the Orders admin and updated the status from Payment Receoved to Completed and then back to Payment Received.

In the Files tab, the two files are listed. However clicking on one of these links gives me this error message: You have downloaded this file too many times. Please contact the site administrator if this message has been received in error.

Both files (for the one product) show as having 0 downloads each. This is all with the latest bazaar checkout.

EDIT: Actually setting the Number of Downloads limit (in this case 100) fixed the problem. It seems you can't leave it blank at this point.

EDIT 2: After starting the download, the number of downloads displayed under the Files tab has not changed to reflect how many times I have actually downloaded the file. It is stuck at 0.

Sorry, another update, as I am playing around with this module. I noticed that the file products are attached to users. Is there a reason why this was the preferred method? I'm wondering because, as I've mentioned before, we have 16,000 or more customers (no joke) and if we add one file to a product that everyone has purchased (and they are out there) that would mean 16,000 queries to retroactively add a product to each order that exists.

Of course the retroactively purchasing aspect doesn't seem to work on my test site anyway so I can't really test properly. I'll be sticking to my current file product module but will be glad to continue testing the uc_file method of things on a separate site.