I just noticed the last SVN Flake is on par with Monkey's Audio
I downloaded FL Studio (again) on Windows just to play around with it, and generated a 192kHz/24-bit file from one of the demo's (SolidInc - What I Found) which has quite some content at around 80.000Hz. FLAC is on par with Monkey's there. When I lowpass it at 20.000Hz and keep it in the 192kHz/24-bit and encode it with Flake it even outperforms Monkey's.
Original, not lowpassed audio file
Wave: 296,5MB, duration 4:29
FLAC -8: 57,2%, took 43 sec (encoding CPU)
Flake -8: 54,4%, took 28 sec
Monkey's -c3000: 53,4%, took 38 sec
Wavpack -hh -x4: 53,6%, took 856 sec
lowpassed
FLAC -8: 53,9%, took 41 sec
Flake -8: 44,1%, took 29 sec
Monkey's -c3000: 44,7%, took 37 sec
Wavpack -hh -x3: 50,2%, took 187 sec
Wavpack -hh -x4: 27,0%, took 842 sec
Of course this isn't an in-depth analysis, but it shows that it is indeed a problem with the reference encoder, not with the FLAC format. As you can see, Wavpack's custom filters compress surprisingly better.