I discovered the source of the problem I had. Not a problem with Easy Populate at all, but something that may want to be added to avoid problems.
By default, OSC creates the database with character limits (32 characters for a category name). A few of my sub-category names were longer by one or two characters, so they were being truncated and causing Easy Populate to not recognize them as category name together and therefore giving me duplicate categories. A simple check could fix this from being a problem.
Good work on Easy Populate, works great!