If you applied for a PR renewal on Jan 1st 2009, they will go from the 5 year period from Jan 1st 2004 until 2009 or if you became a PR later than Jan 1st 2004, they will go from that date. If you have applied to renew your PR, they will not consider time you stayed in Canada after that where you could meet the residency requirements. By applying, you have basically waved a big red flag at them while shouting "LOOK AT ME, HERE I AM, I DON'T MEET THE REQUIREMENTS, PLEASE COME AND GET ME" so that is what they will do.
Some people have successfully withdrawn their PR renewal applications in such circumstances and some have even been offered to do that during their RQ interview so it seems that immigration may be forgiving. If you tell them to forget your application, they may sweep it into the bin and forget it ever existed and you can then apply again after you have met the residency requirements. I am not saying they will do this in every case but I have heard of it.