Interesting. I contacted support about this, and eventually found out that the cracks only appeared in my somewhat outdated version of VLC. With the new version, everything sounded fine at first. There were still cracks in one place, though. But I thought they were due to the player, as before. I hope this isn't just converted MP3s now :)
Feel free to run the files through Spek and you'll see they reach into the 22 KHz range. MP3's and MP3's converted into FLACs won't :)
Judas your answer is very misleading :
an MP3 has its high frequencies cut-off (it's the nature of the format -> lossy)
a transcoded MP3->FLAC will display the same cut-off frequencies (i believe it's what you wanted mean or i missed something ?) , except the weight will be much more important.....
because offering transcoded mp3 into flac it's big a NO-NO >.<