PwnageTool has just been updated to 4.1.2 by the iPhone Dev Team. This new releases includes bug fixes involving Cydia as stated below:
[Update: Version 4.1.2 should fix any issues that OS X 10.5.x users were seeing.  You only need to run this version if you’re at OS X 10.5.x and were seeing Cydia errors]
pwnagetool
PwnageTool 4.1.2 will jailbreak the following devices on iOS 4.1: