Channels are configured in the services-config.xml file, and
generally referenced in the other configuration files. In the
messaging case it is messaging-config.xml.
This configuration information is compiled into the resulting
swf. The config compiled in, is specified by a command line switch
-services during compile.
In FlexBuilder this is setup with the project, when using the
web tier compiler this is automatically configured based on the
webapp running. It could be that FlexBuilder isn't including the
services-config.xml in a subsequent compile; by default it doesn't
track changes to those files, so you have to force a rebuild
inorder to get any configuration changes into the compiled swf.
Are you making changes to destination names and then having
this issue?