There is a bug in Subsonic for where transcoding a file from a low bitrate to a higher bitrate. See:
http://forum.subsonic.org/forum/viewtop ... 1&start=15
Sindre already knows about it, and it is in the Backlog secton of his todo list at:
http://subsonic.svn.sourceforge.net/vie ... n/TODO.TXT
So unfortunally it is not on his todo list for version 3.8 yet.
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In the mean time the only thing you can do to resolve this is to either not use transcoding, or you can set the bitrate limit lower than the bitrate of the file you playing. But that means you will get less quality then optimal on those tracks and other tracks you play.
E.g. If you have a 64 kbit/sec wma file that is transcoded to mp3, then you will need to set the bitrate limit to 64 kbit/sec either in the global bitrate settings, the per user bitrate settings or in the per player bitrate settings.
Another solution would be to use an external player that do not require transcoding at all. For instance the VLC Media Player. If you do that, you will need to turn off the transcoding for that player for the formats that the player do understand natively.
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Another solution that can be usable if the problem isn't with too many files and that you can stand the minor quality reduction on the files, you already will have that quality reduction btw, you can use a program like MediaMonkey and transcode the files to say 128 or 160 kbit/sec mp3 files. And use those instead with Subsonic until Sindre fixes the problem. Just keep the original files as a copy, then when Sindre fixes Subsonic, you can swap back to the original files.
AFAIK there is no other solutions at this time.