I think I know what you mean though it's not just about large and small.
PowerPoint makes fairly arbitrary decisions about which shape should move when you align.
With 2010 one solution is to use the smart guides. Manually move the large shape when it centre aligns you will see a smart guide appear.
Better but not free we were annoyed by this too and have a cheap addin which adds a patch to make the standard align tools behave! Less than $20. Trust me you'll wonder why they didn't always work this way!
http://www.pptalchemy.co.uk/anchor.html