Ok I think I understand. The Beta-keto ester has a much lower pKa then the alpha proton of the original ester so the base would much rather rip off that second proton, and form the resonance stabilized Beta-keto ester anion. This would lower the concentration of the Beta-keto ester, effectively driving the formation of it. This ties in nicely with your discussion on Le Chatelier.
Thanks for your help.