The 4.1 tracks do play fine when I set the DSP Channels to 5.1, but that means I have to change it back to Source Number of Channels for stereo music (most of what I have) since I prefer it in 2.0 rather than 5.1 - I don't like either the center channel or surrounds for most 2 channel music.
Some audio drivers don't recognize 4.1 as a valid format, so it's not surprising that it won't play as 4.1 but will play as 5.1. There are other allowable formats (like 2.1 and 3.0) that some audio drivers don't accept as well.
For best results you should set, in Output Format, Number of Channels to be the number of channels/speakers you actually have (example: 5.1), and then set Mixing to "no upmixing or downmixing". This will resolve your problem with no ill effects.
You won't need to change this setting back when playing 2-channel audio, either. You don't have to worry about the center or surrounds for 2-channel music with this setting. Any channels not present in the source file will output silence.
The only time this setting will be an issue is if the source file actually has more channels than you physically have (like a 7.1 movie played to 5.1 speakers). For that, you need downmixing or the sound in the extra channels will be lost.
However you can get around any issues by using ZoneSwitch to automatically apply different DSP rules (like output format and mixing) based on things like the type of media and source number of channels.
Hope this helps... Good luck.
