pywallet will only help you to retrieve/dump your private keys in bulk. You'll still need to find a way to import them on a new wallet, beacuse AFAIK pywallet only let's you import 1 private key at a time.

BTW, could you do one small thing, just to troubleshoot?
Can you rename your wallet a and let the 0.6.1 client create a new wallet.dat and try running that newly created wallet on the 0.7.2 client, just to see if it works?
Or maybe you already did that