I've found that the default settings work pretty well for the most part, but then again, I'm not fully aware of your particular installation history and what you have or have not done to SS that may affect performance.
My suggestion would be to start with a comletely clean installation of SS, which would include deletion of the settings directory - C:\Subsonic on a Windows install and usually some sort of \var directory in Linix installs.
There is also the chance that we can pinpoint the problem and fix it if you can give me enough specific information such as the file type(s) that aren't working and the transcoding string that is currently used for that file type.
It's your call as to whcich approach makes more sense to you based on your knowledge of how "clean" you think you SS installation is.