File sizes comparable to flac reference encoder, typically <5% difference.
There's actually a higher compression setting for flac: -8e. It reduces the difference to a few kilobytes, which is probably just the file format or tags or something like that.
FLAC 1.3.2 creates a 1,75% larger file that the java implementation, which is quite a bit.
I have bit-compared the files and the output is the same.
What is possible (and probably likely) is that there is something "weird" about this file that happens to trigger this, and the vast majority of regular files will not show this. Then it becomes much less interesting.
I would also agree that 1.75% is pretty significant, especially if that's referenced to the original file size (not the compressed size).
flac.exe -8e javaflacencode.flac --output-name flac1.3.2encode.flac2177 KB flac1.3.2encode.flac2169 KB javaflacencode.flac
I also noticed that the reference encoder (flac.exe) uses fixed block size, maybe this is the real explanation?