Are you using last revision? I had that problem when i was using r38, after updating it worked and now it finds the isos in the folder.
You mention using the back port for the HDD, what he meant was that the controller must also be connected to the back port because some people uses both back ports for the HDD (for power and data) and then try to use the controller in the front ports, which is not supported yet.
meta.xml include the app's description, BUT it can also include some other data that it needs/can use when it's loaded. Nintendont has an ahb_access tag, and LoaderGX uses no_ios_reload and some optional arguments as well. So my point is that you shouldn't say that file is not important "because it only has the app's description". If possible you should always have the meta.xml for your apps, just in case it needs it.
Now, if using a different controller didn't work, and you think it's because of the game, try downloading the iso in case your rip is the problem, and I think I mentioned in my post that you should use r38 IF you have a SD with enough space for the game, if you don't have one, then keep testing with the usb version. But if it doesn't work for you and don't have enough knowledge of programming to help the devs, then just do as me and wait until there's a version that works.