Just came across the same problem trying to make a bad USB...
I tried to run this command in admin cmd
java -jar c:\fw\ducky\duckencode.jar -I c:\fw\ducky\HelloWorld.txt -o c:\fw\ducky\inject.bin
But got this error:
Error: unable to access jarfile c:\fw\ducky\duckencode.jar
Solution
1st step
Right click the jarfile in question. Click properties.
Click the unblock tab in bottom right corner.
The file was blocked, because it was downloaded and not created on my PC.
2nd step
In the cmd I changed the directory to where the jar file is located.
cd C:\fw\ducky\
Then I typed dir and saw the file was named duckencode.jar.jar
So in cmd I changed the original command to reference the file with .jar.jar
java -jar c:\fw\ducky\duckencode.jar.jar -I c:\fw\ducky\HelloWorld.txt -o c:\fw\ducky\inject.bin
That command executed without error messages and the inject.bin I was trying to create was now located in the directory.
Hope this helps.