When I seek in FLAC files, I hear a choppy sound and then it plays normally. I wouldn't have brought this up, if I wasn't aware that the reference Winamp plug-in doesn't have such a problem. Using DirectSound as output, Pentium II Celeron 400 MHz, W2K+SP3, DirectX 9.0a, default settings for Foobar.
edit: The output method doesn't matter, all of them cause choppy sound. The FLAC files I'm testing were encoded with default flac.exe setting.