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.