For me it happens also with mp3s in loudly recorded tracks depending on the encoder used (the ones exported directly with cubase tends to have that issue) but you can also simply use WASAPI, then you avoid it as well, no matter mp3 or flac. That's one of the reasons I recommend to use WASAPI output as it handles loud recordings fine.
There's been those cases (doesn't have to have the DH config enabled) where DirectSound would be aprox 25%-35% more silent than when using WASAPI, it's like very big difference. xD
Edited by RPGWiZaRD - 3/3/13 at 9:19pm