Thts probably explains why my directory structure ends up being slightly different. But it doesn't explain why loading the audio files gives different results and it then crashes when it attempts to actually play some music...
I added a bit of debug output and commented the exception out so it doesn't fail when loading the first file...
Loading audiodata: audio/music/Trials of The Pharaoh Gameplay1.ogg; frames: 6947987, channels: 2; sampleCount= 13895974 numread 6947904; frames 6947987 Loading audiodata: audio/music/Trials of The Pharaoh Gameplay2.ogg; frames: 5226003, channels: 2; sampleCount= 10452006 numread 5225920; frames 5226003 Loading audiodata: audio/music/Trials of The Pharaoh Gameplay4.ogg; frames: 4030355, channels: 2; sampleCount= 8060710 numread 4030272; frames 4030355 Loading audiodata: audio/music/Trials of The Pharaoh Intro.ogg; frames: 4923923, channels: 2; sampleCount= 9847846 numread 4923840; frames 4923923 ... ALSA lib pcm.c:8526:(snd_pcm_recover) underrun occurred