Ok ... in a final struggle to at least have something to show at my talk at ApacheCon I dug really deep into the compiler and noticed one thing:
There's a class called: JSSharedData, which contains a set of public static variables for containing the state of a compilation (I guess). The problem is that the values inside are set by the constructors of the compilers ... well actually just MXMLJSC but as COMPJSC extends from that also from that. In the FlexJSToolGroup I create an instance of any tool the group has. First one of COMPJSC and then MXMLJSC. So when creating the MXMLJSC instance all the static global variables correctly initialized by COMPJSC are overwritten by those of MXMLJSC. The reason I didn't notice this, was that in my last attempt I only used MXMLJSC in my examples from Flexmojos. This "one state that's shared between compiler instances" is really bad as the VM isn't destroyed during the build, this means that eventually settings from one module could leak to another module. I guess it would be absolutely impossible to track down problems like this. "public static"-Variables for maintaining the State of an instance of anything is super-duper-ultra-bad ... we have to change this. Chris