I had problems converting BBC streams automatically with Replay AV. But since installing Replay Converter 3.0 beta the conversion of Real Media/Real Audio audio streams from BBC has been working great.

How to convert audio streams to m4a, m4b (and add to iTunes) after capturing them with Replay AV

• In the Replay AV open the Properties window for the show which files should be converted after capturing.
• Select the Basic tab. Select the format you want to convert to (such as m4a, m4b,...) in the After recording, convert to combo box.
• Select the Output tab. Mark the Keep copy of the original file after converting check box (if you wanna keep the original recordings).
• On the Output tab check Add to iTunes library if needed.
• Click the OK button.

You should also change the DirectShow options of the Replay Converter

• Launch the Replay Converter
• Hit the Options button. Hit the Audio conversion options button.
• In the Audio Conversion Options mark Real (.ra) and Other checkboxes to use Direct Show when converting from these audio formats.
• Hit the OK button. Hit the OK button.