Either one of the factors may affect either balance:

• There is a double spend against one of your accounts
• Some transaction might not have yet been included in a block and one program does not see it yet
• There can be an error in one of the programs that skipped over some transactions. In case of the client, you should try rescanning the blockchain to make sure all data is properly extracted in case you suspect an error

You should make sure your client is fully synchronised and all your transactions have at least one confirmation.

You should generally trust the place where you issue your transactions from to have an accurate balance of your outgoing transactions, and blockchain.info for the information available everywhere else.

As it turns out, the import did not pick up all my addresses/keys. By comparing the output from pywallet --dumpwallet and the blockchain.info exports I was able to identify the missing keys and add them manually. Both balances match now :-)