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?
Did you make sure the required extensions as described in the blog post are installed in the headless buckminster? If you did, then it may be that buckminster uses a different "entry point"/"call mechanism" to invoke the PDE functionality. In that case (i.e. if that does not help), I suggest you log an enhancement request in the eclipse bugzilla for buckminster.