After a few tests with the encoder I have noticed that some of the files it created had a nasty DC burst near the end of the file that can be heard when played with either Foobar or Winamp. It has been confirmed by checking in an audio editor

The funny thing was that it was not happening with all the files I was feeding the encoder with. After having thought hard for bit I have realized that the lowest common denominator was that the files the encoder would add some DC burst to were the file created with FL Studio. This program adds some RIFF sub-chunk data to the files it creates("Created with FL Studio 5", or if you specify it when rendering it adds info that can be read by Sonic Foundry Acid).
I have then created some small clips in FL Studio to test with the encoder and each time the DC burst was here.
Knowing that the FLAC encoder removes the RIFF sub-chunk data when encoding the files, I have tried encoding the original file created in FL studio with the FLAC encoder(which indeed found RIFF sub-chunk data that it removed) and then decode it back to wav to try to feed the Helix encoder with the decoded FlAC file. It worked as I expected to, the encoded file had no DC click at the end.

My conclusion is that the encoder will produce a DC burst at the end of the file if the Wav file contains some RIFF sub-chunk data. I have tried with various settings, bitrates, HF encoding or not, VBR or CBR and it constantly happened no matter what when the RIFF sub-chunk data was present.
I would gladly provide the devs with files created containing RIFF sub-chunk data if needed.
J.
