And which FLAC plugin are you using?
Note that in_flac does not come with the default Winamp distribution
and playback support is currently only available via an unsupported 3rd-party plugin.
Native FLAC support is planned for the next Winamp release,
and I certainly can't reproduce the problem with the current internal beta version.
[moving this from Bug Reports to Tech Support - BR is not for reporting issues with 3rd-party plugins]