Ah! Thanks for figuring this out. I'll be honest, I don't do much testing of Minim in Linux even though I do have an Ubuntu install. Here's what I think is probably going on:
Vanilla JavaSound on Ubuntu probably only has one little-endian output available, so when you try to load two little-endian files, the first one snags the output and the second one is left high and dry. The Pulse audio library probably has some service provider stuff in it that makes a Mixer available to JavaSound that can handle more than one little-endian output, so no worries there.
I just took a look over the code that generates these errors and as far as I can tell, I'm doing the right thing. I generate a DataLine.Info object using the AudioFormat of the file you are trying to load and then ask AudioSystem if that kind of line is supported. Then, if you've set an outputMixer for Minim, I ask for a SourceDataLine from that, but if you haven't, I ask AudioSystem. I'm guessing you haven't set an outputMixer, so it's probably asking AudioSystem in your case. That should be fine, it would query all of the Mixers the system knows about and return a SourceDataLine from the first one that could support it.
The annoying thing here is that one might expect AudioSystem.isLineSupported to return
false if none of the Mixers actually have a SourceDataLine available for the format in the DataLine.Info, but it probably considers "support" to be different from "is one available right now".
I'm curious to know if there's anything I can do in Minim to remove the need for Pulse in this situation. I'll make a note of this issue and have a look at some point.