When starting stendhal 0.66 for the first time (upgraded from 0.65), it checked for updates and it found the patch to go from 0.65 to 0.66, even though 0.66 was already installed.
Deleting the files in the equivalent of ~/stendhal/jar solved the problem. This is still a bug however and should be fixed.
OS: Windows XP SP2
Java: Sun JRE 1.6.0_03