Well, I don't want to sound like an evangelist, but foobar2000 plays FLAC just fine, with gapless playback and whatnot and the interface is quite the opposite of Winamp's.
Ok well an initial install I like that its a lot simpler than WinAmp, but one major problem is an initial scan of my local music library and it only found 784 songs when in fact I have 4733 showing in winamp. Now they are a mixture of mostly FLAC but some MP3 and WMA, also a lot of in sub-folders. Does it not handle sub-folders do you know?
It definitely handles subfolders. I'm not sure what the problem is, to be honest. All I can think of is wrong settings in the "Media Library" preferences.