Flac compressed definitely sounds worse than Flac uncompressed... The difference is not huge and may possibly be dependent on your hardware quality level but you're perfectly right here.
I've just compared flac uncompressed with wav (several songs, same analysis by Jriver)... If there is any difference, then it is REALLY small and not clear almost all the time.
I am not 100 % sure if it is not a placebo effect only what I am hearing but in high pitched sounds (orchestrations, synths or cymbals etc.), wav offers a bit more natural feeling IMHO. I've got this intention from every song I tested but in one of the songs (Unleashed from Epica), I spotted a mini-section where a well-profiled high pitched sound could be very helpful in distinguishing any differences... I did a blind test with only two tracks in playlist (flac uncompressed Unleashed and wav Unleashed, both converted via dbpoweramp, same version) and listened to these two tracks several times with closed eyes to lost any intention which one is currently playing (I of course tried to move with keyboard arrows before to ensure myself that I will be able to switch tracks properly :-) )...
Result? In this section, it was really well possible (suprisingly) to spot a difference so when I was sure that I was listening to the better version I just opened my eyes and saw the WAV FILE... Oh yeah.
I am not a scientist... This is just my2cents. Hopefully it can help.
Info: Jriver media player with WASAPI (not event style), Auzen xplosion 7.1 DTS soundcard,FiiO E9 amplifier, Denon AH-D7000 headphones.