Help Ringtones problem

Not sure if it has something to do with the Kyocera Rise in particular but I haven't found anyone with a similar problem after searching :/
I have a 16gb microSD in mine with TONS of music and most of it is either in the folder "download" (which was auto-created by the phone at some point) or "Downloads" (made by myself) and for some reason the Android System's ringtone menu thinks every song (.mp3, .flac, and .m4a's are all I have) in my Downloads & download folders is a ringtone. This makes searching to find the ringtone I want a largely bothersome task, and I was hoping someone here might know how to fix it. The ringtone maker app I use made a convenient "media" folder with subfolders for ringtones, notifications, etc, and I would like to just use that folder and possibly another one made by a soundboard app, but I can just move those to the media folder if necessary. I'm assuming this all has something to do with the way Android handles apps that make/assign ringtones in custom folders, but I'm really not too acquainted with Android beyond advanced usage of it (know nothing about Python or how the coding works, all I've ever done with coding is some visual basic, java, and c++ rudimentary classes in high school)

FYI I have rooted the device and am otherwise pretty adept with technology so even if it's really complex, I'm sure I can do it with a little instruction :D
Also, some general info on the phone that might help:
Android 4.0.4
Kernel version = 3.0.8-perf, release@release#1, Sat Jan 12 21:43:40 JST 2013
Carrier = Virgin Mobile

tl;dr - phone thinks everything is a ringtone despite having specific ringtone folders made by apps, pls halp :(