I've ran into the same problem here :
http://www.hydrogenaudio.org/forums/index....ST&f=11&t=9750&SoundForge added some "metadata" (date of recording, name of the program...) at the end of the wav file, that caused
1) The SoundForge file to be bigger than the Flac decoded one
2) Mppenc 1.15r to bug trying to encode the SoundForge file
I've examined the two files with an hex editor, and checked that the amount of audio specified at the end of the wav header was the same in both files. SoundForge itself displayed the same amount of samples in both.