Vogone I is like all other vocal eliminators. It uses the fact that any sound that is equally loud in both the left and right channels of a stereo file can be totally and cleanly removed.
The problem you are hearing is called flanging. This is coming from the fact that your left and right channel sounds are changed somehow.
[li]If the files were processed with MP3, the channel audio is damaged and will cause weird sound processing.
RECOMMENDATION: Don't try to vocal eliminate MP3 processed files. 
[li]If the channels are delayed very slightly from each other this can cause phase cancelation which can amplify some frequencies and attenuate others.
The result of either cases above is that phase cancellation is happening in areas other than the center. The resulting processed file will usually not be usable.