The 1.21 BC was in a single "chunk". When you sent 0.01, you made a transaction with one "in" (the "chunk") and two "outs": one sent 0.01 to whoever you sent that to, and the other one sent 1.20 back to you as "change". This second "out" was sent to a brand new address that you just generated. Since your old wallet.dat doesn't have the keys to this new address, you don't see it.
That's very odd. This is very similar to doing a backup and restoring it later. if that actually happened isn't there any way to find out what is this new address?
What is odd?
If a writer has written 200 pages of his book and have it in a wordpad-file. Then he removes that file and open the last backup that only contains 50 pages.. well it will only show 50 pages and not 200, this is not odd. Make a backup everytime you use your wallet and save the old backups just in case.