Thanks for testing this out.
Are you saying that you are able to click on the COGS menu, it shows the 3 options, but when you try to select one of the options, Ajax runs, and the option returns to the initial value ("No")?
If you are actually testing my fork, the COGS menu is not Ajax enabled, and operates as a standard options menu, so Ajax should not run (you should not see the Ajax icon pop up when changing the value).
Note that the original pull request did Ajax enable the COGS menu, but that has been since simplified in my fork so that now the recosting is not run until the order is processed.
I do use this feature on a frequent basis, although for simplicity, only on invoices where the freight and other excess charges appear on the invoice itself. If the freight appears on a separate invoice, I don't try to wrap it into the item cogs as I suggested.