Something changed between the 1.0.5 and 1.0.6 releases (probably in the EmbeddedFileDependency functions).
Running the Alchemi_jsub.exe utility using the JobAPI example in the SDK comes back with the output files as 0 length files. When I checked the threads via the Console they were labelled 'Dead' (priority -1) but the application was still labelled as 'Running'. The same thing happens using ALchemi_jsub to submit the Blast-demo job to the grid.
I also tried it via the the GridReverser.exe example and it didn't work either so it not something specific to the Job Submitter.
I also have the same problem...