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?