Not sure if I'm following all those dates, but let me give a general response. You're allowed to extend the performance period for any credit back 24 months from the latest performance period end date for your project. So if all of your credits end on January 10, 2011, you can claim measured performance back as far as January 10, 2009.
When it comes to the Statement of Energy Performance from Portfolio Manager, those summaries are generated for a specific 12-month period. You specify an end date and the tool gives you an Energy Star score associated with the preceding 12 months.
So, if you want your SEP to align with your performance period, I'd suggest generating a new SEP using an end date that matches or closely matches the latest performance period end date in your project. Remember that your credits don't all have to have the same performance period end date - as long as they all fall within a shared 30-day window, you'll be fine.