There should not be a difference in volume between Flac and WAV files containing the sample audio stream.
Some possibilities for the difference you heard:
1. Replay Gain: when you rip a CD, MC or another ripping program can analyze the audio stream and record in a tag in the music file some information about how loud the audio stream is. When the file is played, MC or another player could adjust the volume based on the Replay_gain value. Some info:
http://wiki.jriver.com/index.php/Replay_gain#Auto_Analyze_during_RipThis explanation would apply if
- the WAV file didn't contain a replay_gain tag and the Flac file did.
- The MC setting to use replay_gain to adjust volume during playback was turned on.
2. Normalization: MC or another ripping program can adjust volume before the audio stream is stored in the music file. This is a permanent change. Some info:
http://wiki.jriver.com/index.php/Encoding_SettingsThis explanation would apply if
- Normalization was applied when the Flac file was created and not applied when the WAV file was created.
In both cases, changing a couple of settings in MC (or another ripping program) will remove the difference.
Other people may have additional possibilities to suggest.
Bill