A couple things sound weird...
1. "2.0" by definition is no sub(s)... (that's what the 0 means).
2. Sometimes 1 sub plays, and sometimes 2 subs play.
For #1, I would reread the manual. Is "2.0" stereo, or more like stereo direct? Make sure you are not selecting a "direct" mode. Also, what is your sub selection? LFE? LFE + main? How about your crossovers? Are your front speakers set to "Large" or "Small"?
For #2, I would check how the subs are hooked up. Do your Yamaha have 2 separate sub outputs? Are you using a Y-splitter?