I am having the same issues. I noticed its with my USB sticks with FLAC files on it. I tried using a 2.0 USB stick and still problems. I called Pioneer and they said it might be the USB ports, but that doesn't make sense if it reads it and locks up. Then I have another car and I installed the 4100nex and it has the same problems. It's a software issue for sure. Pioneer needs to fix this. I have never had this problem with other headunits.
Anyone else have any luck?