There were some issues, when I tried to run a small example, that was printing the audio to stdout in nodejs for testing. It was producing awkwardly distorded audio. It turned out, that nodejs somehow messed up the output and the libraray was working correctly.
manx, as you just found out, there is a libopenmpt repository. All my changes are in these
two commits. I only modified the build system.
The emscription version is 1.16.0 (commit 326078dbfd2d1b412546dffef81964c3d2ca125d). I compiled it myself quite a while ago, but it already uses the fastcomp backend. There is a good guide in the emscripten wiki (a quadcore cpu is reccommended

).
I haven't run the tests yet, but i'll try to do so.
I will also look into your bug, strangely it works for me in Firefox and Chrome. Unfortunateley I am stuck with Firefox 30, as my internet connection is broken and I'm online via my phone.
Update:
I ran the tests. The TestITCompression fails. This is what it tells me:
Test: test/test.cpp(88): TestITCompression:
Test: test/test.cpp(88): TestITCompression: FAIL
FAIL: Test: test/test.cpp(88): TestITCompression : '
TEST ERROR: exception: vector
TestLoadSaveFile fails too. This seems correct to me, as you can't do file io in regular javascript. The tests were run in nodejs.