Thanks very much to you both for your support.
Rarkenin, The Blockchain on my PC is up to date and both copies of the wallet are fully in sync with it. I swap the wallets in the .bitcoin folder, one includes the 40mBTC transaction and the other does not. The missing transaction is in the middle as there are older and newer transactions.
Kouye, Just discarding the wallet that is missing the 40mBTC transaction may solve the problem but not the Mystery.
You're not the first one to report a -rescan failure.
The mystery might be explained by the way QT keeps track of balance internally.
He does not care what unspent outputs are used when you send coins, for example, it'll always use your default address to keep track when you send coins (meaning you generally have a negative default address balance, and all your other addresses have a balance as great as the greatest one they ever had). The way QT computes the balance is just local, it basically does not care about matching the blockchain.
Check the result of
listaccounts
Which, I beleive (not 100% sure, though), is used by QT to compute the current total balance
And check the result of
listunspent
By comparing those, you might find where the diffence is.