I figured I should post my findings in case someone searches for this problem in the future. In short, I moved all the media off my 1TB fat32 USB drive, removed the device from linuxmce, reformatted it ext3, let linuxmce add it as a new drive, then moved my media back. This has completely resolved the weird pausing/freezing issues I was seeing on my MD. Live TV (via Myth), media playback, even MD boot time and menu navigation are all far better now and media playback is smooth and reliable again.