SSH Connection does not close resources

My Host env : Windows 7 - 64 bit
My Remote env : Ubuntu 12.04 - ARM v9

I am using WinSCP for remote program triggering. My program reads the streaming data from USB port. I trig the program, works successfully and i can see the output. When I try to stop the program, I cannot stop the usage on the remote environment and I keep getting resource is not ready errors while trying to execute the program again.

Can you please provide more details about your workflow. I really do not understand what is this about. Does your script upload some Java program and then execute it? When do you get the error? Or the second run? How do you stop the program? Etc...