I am using a headless version of Buckminster, v3.6. From what I had read, by updating to Eclipse 3.6, the PDE environment will build AspectJ projects, if you include certain configuration in the build.properties of the AspectJ project. The information on this can be found here:
http://contraptionsforprogramming.blogspot.com/2010/03/ajdt-pde-builds-redux.html
It seems that this does not matter when using the headless Buckminster for the build process, as it does not take this setting into account. Has anyone managed to get a headless Buckminster working to build a plugin containing AspectJ aspects?