I'm not quite sure what you have done and so what you are asking...
You have a Java application that calls out to an executable shell to run PGP Command Line, and you are wondering if there are any differences between 10.0 and 10.1 that might cause your application to work differently (or not at all)? Is that correct?
We very rarely make changes to Command Line that might have any effects on scripts that call Command Line. The only exception is if we feel that the existing behavior is not as secure as it ought to be -- e.g. we may decide that we need to return a better error code in some circumstance.
I do not believe we have made any such changes between 10.0 and 10.1. It should behave the same for you.
Regards,