Automatic Crossfaes disappear when I Rebuild the layers

Ok I'm working on a live concert for a major client and things are going swell until after many hours of working and editing and re-tracking bits and pieces with many tracks and layers, to my chagrin when I rebuilt the layer all of the automatic cross fades vanished. My client I very very upset and swore he will never do another project with me again unless I change to anything but sonar. It would have been ok if the crossfades were not audible but they are! Help