FYI, just in case you aren’t aware of this, there are a lot of issues pertaining to audio formats besides whether something is a WAV or not. I apologize if I am mentioning something you already know, but the posts you gave allow an ambiguous interpretation.
It can be stereo or mono, and the bytes can be in either little-endian or big-endian order. It can be 16, 24, or 32 bits encoding. And concerning frame rates, I think (I could be wrong) that 44100 is the maximum supported by Java, but some DAWs are now working at 48000 or 96000 fps. If any of these parameters are varying between the samples, then the formats could be an issue.
I think I also had some trouble once when I designated the ‘compression’ option when generating a jar in Eclipse for the resource files. This might make a difference as well, though admittedly WAV files are pretty large if they aren’t compressed, and this might make using some sort of compression (at some stage or another) mandatory.