A: 

I have 0 experience with Air, but this reminded me of a Java issue I once spent some time figuring out. I don't have a suggestion on why the scanning doesn't work, but I think a stack trace would be your best friend right now.

I'm guessing you're relying on this line to capture and display it?

nativeProcess.standardOutput.readUTFBytes(nativeProcess.standardOutput.bytesAvailable);

However, you are writing IOExceptions to System.err - is there a nativeProcess.standardError you could read in Air? Alternatively, output everything to System.out.

Lauri Lehtinen
I changed the exceptions to output to stdout and added a listener for stderr on the Flex side. Still Nothing back.
Donny
Does your AIR app display the "Start"?
Lauri Lehtinen
Yes. If I take out the SourceManager line then the Java app just echos back whatever it receives on stdin
Donny
+1  A: 

When calling Java add this -Djava.library.path=location_of_dll to the command line

Romain Hippeau
Added the absolute path as a command line argument just like that. Still nothing.
Donny
You totally solved it. I misunderstood and used C:\Program Files\JTwain\AspriseJTwain.dll when I should have simply supplied the directory, C:\Program Files\Jtwain. To be clear to everyone else, the fix was to add the line arg.push("-Djava.library.path=C"\\Program Files\\JTwain"); to my code.Thanks a ton!
Donny