Great, I'm glad you figured it out. Kudos to the person installed PyRx on your computer; very smart move. I haven't had a chance to make any updates to Windows installer for years - http://sourceforge.net/apps/trac/pyrx/roadmap
That's why there might be bugs in Windows version that might have already been fixed in the latest Linux version of PyRx.
Regarding the question about adding hydrogens: yes, please do add hydrogens before making pbqt. Ask 3 scientists how to get the right results in docking and you will get five different answers.