The following are major known bugs in the current (1.3.1pre1) release:
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If you use the --replay-gain option with flac, but no --padding/-P option, only a very small padding block will be created. The workaround is to always use a -P option when using --replay-gain to make sure the correct amount of padding is added.
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When encoding to Ogg FLAC, the progress indicator is broken
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When encoding to Ogg FLAC, the number of seek points is limited to 240.
The first two have been fixed, these fixes will be incorporated in the next release.