I'm having some trouble with Flash Builder 4.5 and Flex SDK 126.96.36.19928 with AIR 3.0 RC1. Flash Builder does not appear to compile modules into the location set in the "Edit module" dialog.
The screenshots below show that the output path of a module is set to a specific folder, yet Flash Builder compiles the module into the default sub-folder.
#1. Project properties showing application modules
#2. Dialog showing the path to the module. Not the "Output SWF" location. The default location is the same as the package namespaces, eg: "d6/v3/banners/Banners.swf". After removing the path the module should compile into the output folder (set to bin/debug), however as the next screenshot shows, the module still compiles into the default sub-folder.
#3. The module is compiled into a sub-folder of the output folder, instead of into the "root" of the output folder.
#4. The output folder contains only the main application, with a sub-folder for the module.
#5. Project pproperties showing the output folder.
There is a workaround - move the module source file into the "Default package" in the package explorer.