I believe the source code is either C or C++.
And sorry, I think I didn't explain clearly - it's not these midi files from the conversion that are bugged (or maybe they are too, I didn't check closely enough). I'm referring to when playing the actual game in DOSBox - I have no idea if the same happens when using General Midi on real hardware, as that option didn't work on my real hardware back in the day, and I don't have real hardware that L3D could run on now (I could perhaps try a virtual machine running DOS though, but that may not be 100% accurate to what real hardware would have done).
It's most noticable on the standard Computer track (towards the end), but there's also more subtle stuck notes on the standard Space track too, and a few others.