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I don't think there's much to be concerned about.  Here are the current votes by project: 

Curse of Castle Killem : 12 
G.T. : 10 
The Future: A Right To Arms : 9 
Assaulted : 9 
Story Trigger : 8 
Project Cybernut: 7 
Taffer : 7 

Those aren't votes, just the amount of people who have rated the game, correct?

How exactly is scoring determined at the end of the ratings period? Is it an average of the ratings?

Yeah, and given mine requires people know how to set up an emulator it makes sense that it's on the lower side.