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It seems that beta 2472 doesn't properly name files when "create folder structure in output" is deselected. With most of the files I've tried, it just names them "0" and overwrites the previously encoded files. Another small issue is that the latest beta doesn't include any encoder information in the tags. The replay gain tags don't seem to be working either. I ran into all of these issues using the x86 version with qaac if you're wondering.
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Thanks for the report.
Tool tag is overwritten because a different way of tag writing is used.
Can you post the logs of a failed encode? Under logs window "Create log.zip" will create log.zip in desktop.