I have a bit of an issue when I export raw tracks from a SONAR Platinum project.  If I have punched in and recorded over a section of a track, the exported raw track will include the original muted part mixed with the part that was punched in.  Am I missing a setting or something that would fix that? 
 
I basically use the preset for Export Raw Tracks with no FX, the only change I make is from Stereo to Follow Source, so my mono tracks stay in mono.  None of the options look like they would be exactly what I need to ignore muted clip takes, unless they just didn't word it as expected.

Could it be something in your recording preferences?
 
See this thread: http://forum.cakewalk.com...th-takes-m3439634.aspx

I've had this happen, basically the original is a muted clip on the same track. Make sure the mute status checkbox is checked when you export.

OK, I think I saw an option for Track Mute, but was looking for an option for Clip Mute.  I'll try that.  Thanks!