this might be something simple. Try these steps first, to rule out the basics.
1) If you have WBFS manger open, then close out of it.
2) Disconnect and reconnect your USB drive to the PC - ensure the PC sees the drive letter again
3) Launch WBFS manager again
4) "Load" your wii USB drive - you should see all the apps you currently have on it.
5) Locate, on the right side, the .ISO file you want to load
6) Click on Add to drive button
This 'should' be the process to transfer apps. I also just happen to transfer punchout. It took short moments.