I can not manage to play the file except downmixed to stereo. But it seems to contain 3 x 6 sweeps allright, except I could not hear the sub sweep, but a pause instead (maybe the lower part of the sub sweep was there but I couldn't hear it).
@Dixter: are you sure that is not what's happening in your case (for whatever reason): downmix to stereo? And maybe dolby prologic being applied afterwards? The latter could explain that you do get a sweep in the center, but the rear L and R sweeps are going to L and R front (I assume you mean fronts with L and R).
If
@SobiC can hear the 3 x 6 sweeps correctly then I assume the file is ok but it is just a matter of how to play it back correctly.
(I have never had 5.1 channel flac or wav files before, I have to figure out first how to play them.)