Nothing weird with the different md5 sums you got. Normal md5 check only compares how the files "look" from the outside. The three files look totally different despite having the exact same music in them, hence the different sums.

You're probably mixing this up with md5 sums created by Shntool. That goes beyond the looks and checks just the uncompressed audio part of the files. It ignores the compression used, tags and all that. Hence, you get identical sums for APE, WAV, SHN, FLAC etc files that have the exact same music in them.

If you use foobar2000 you can use the 'Bit-compare tracks' to check that everything's ok.