I'm not home to check my work, but I did some searching on this before dean70 responded, and I think I found that flac wants the channels in a different order than what dean70 said.
I can't remember, but the LFE channel should be last, and the center should be just above that in Audacity. The LFE is currently the middle (3rd) channel in the 4.1 file you probably have. Move that to the bottom, add a blank mono channel just above it, and change the options of the program to output as discrete channels (default is to combine everything into one channel).
I did this to one track, but have not had time to test it yet, which is why I haven't responded.
I think the channel order should be FR FL SR SL C LFE. I might have the surrounds backwards, but if you do as I described, it will match the layout that I found online for flac files.
I'll report back once I've had a chance to check my work at home.