Xbox 360 not transcoding .avi files

I'm having a problem with certain .avi files not being transcoded when they need to be. The Xbox does support some .avi files natively but not others and Serviio doesn't seem to be able to distinguish between the two so doesn't try to transcode any .avi files.
When I play the files on my laptop they're fine but when they stream they're not being transcoded (I can tell because it lets me skip forward). It plays for a couple of seconds perfectly and then the sound gets quiet and choppy. Almost like it's stopping and starting for a fraction of a second at a time. When Serviio does force transcoding (ie. .mkv files) it works flawlessly regardless of file size/quality so I don't think it's caused by my hardware not being up to scratch. It only occurs on .avi files.
I know this is probably a problem with the way Xbox only plays certain types of .avi files but is there a way to set serviio up so that it will only attempt to play the ones that do work and transcode the rest?
Sorry if I wasn't clear but it's an odd problem to try to describe!
When I play the files on my laptop they're fine but when they stream they're not being transcoded (I can tell because it lets me skip forward). It plays for a couple of seconds perfectly and then the sound gets quiet and choppy. Almost like it's stopping and starting for a fraction of a second at a time. When Serviio does force transcoding (ie. .mkv files) it works flawlessly regardless of file size/quality so I don't think it's caused by my hardware not being up to scratch. It only occurs on .avi files.
I know this is probably a problem with the way Xbox only plays certain types of .avi files but is there a way to set serviio up so that it will only attempt to play the ones that do work and transcode the rest?
Sorry if I wasn't clear but it's an odd problem to try to describe!