Hmm, everything you are showing appears to be correct.
Where are your roms located ? What is the full path to the folder with them ? Sometimes if they are really deep the path can be too long for Windows and it will break command line functionality. I don't believe that is there issue here, looking at your folder structure it looks like you have your stuff organized in a sensible manner.
Unfortunately for me right now it is almost 4:30 am so I have to head to bed but I have passed this thread along to the other moderators and hopefully they can get you sorted out. I will check back in tomorrow.