Tom,
I think there is something wrong with that latest jar file, when I'm using that one I can't restart/start any service that has the PrintSOE enabled, except my empty layout service. And can't make a print.
Edit: Did some more testing. All my services except the layout is based on .msd documents, I published a couple of new services from the .mxd documents and I was able to enable the PrintSOE on them.
My test service without annotation works fine, the one with annotation works but is low quality and the annotations are missing. Is that expected? Is that what you meant with "The sub-annotation-layers are currently ignored."??
In the lyr folder the lyr files seems to be good, there is 0.lyr, 5.lyr, 6.lyr and 7.lyr and all works in ArcMap so the number/names are correct and there's no lyr files for the annotations sublayers.
But the .msd based services are supposed to work with the PrintSOE right?
/Mattias