The biggest problem arises after 100 addresses have been used.  Since Bitcoin-Qt generates random private keys instead of using a deterministic algorithm, the change from the transaction will be sent to an address that only exists in one copy of the wallet.  As such you no longer have "2 copies" of the private key.  You only have one.  Now if you are sending transactions from both wallets, you'll end up with some bitcoins only associated with addresses in one copy, some bitcoins only associated with addresses in the other copy, and some bitcoins associated with addresses in both copies.  The average non-technical user who has been happily using their two copies of the wallet without seeing any issues suddenly notices that the two copies of the wallet no longer have the same amount of bitcoins, but has no understanding of how or why this has happened.  What they do next to attempt to resolve this issue on their own carries risk of losing the private keys from one of the copies of the wallet (and as such all the bitcoins associated with private keys that only belonged to that "copy").