Gavin Andresen - 2011-11-28 20:10:15

The version is 0.3.15.4 beta

0.3.15 is pretty old, and the way you're spending from a copy of the wallet is, I suspect, confusing it.  Pieter updated the wallet code to handle transactions with partially spent outputs a while back.

Try upgrading to version 0.4.1 or 0.5 and running -rescan and see if your missing bitcoins reappear.