It seems that Magento 1.x versions will in fact load any file from the app/etc/ with the .xml file extension. So there is likely a backup of your old configuration that is being loaded and taking precedence. This in depth post goes into some detail about how those files are loaded and interpreted:

The while loop will go through the remaining XML files and load each one. If you’ve ever accidentally copied another XML file into the app/etc folder and had weird things happen, this is the reason for that weirdness. Magento will load ANY file that ends in .xml.