By "file sorter," there are programs out there that will sort your library in alphabetical order if the player does not do it for you.
In my case, I discovered that the limitation to my unit. I went Best Buy and tested my SD card in their display model x930, and it did the same thing. Then I tried my SD and USB in their display AVH-P3300DVD, and that unit (as well as a JVC they had), read my entire library! I got back home and looked at Pioneer's online manuals, to find that although my unit and the "flagship" AVIC-z130bt, allow a max of 300 folders, other units such as the AVH line, and all of the single DIN units allow anywhere from 500 to 6000 folders! I would have never guessed Pioneer's two top of the line models would have such limitations. The dealer I purchased from will not allow an exchange, so now I'm stuck. I think I will reorganize the folders on my SD card, so that I have no album folders, and I will just use the SD card on random tracks/files. If I want to play certain albums, I have just been streaming through by phone's bluetooth, since I have my complete library on my Droid phone.