I had the same problem for a year. I eventually found out SCLive clips will sometimes be imported to Vegas as Progressive. Only way to workaround is to kill scene selection and make sure the clip is set to lower field first. Probably not applicable to you if you're capturing with Vegas.

Someone just wrote a script that will do this on the entire timeline; if I didn't find the audio easier to work with as one whole clip, I might go back to scene selection with this.