The Dev Team has just released the updated PwnageTool 2.0.3.1. This version is supposed to fix all of the recent permission related issues and some other minor problems. I'm giving it a try right away and keep you posted.
Here is the direct link from the Dev Team blog. Here's my mirror. Please try the official link first and do only use my mirror in case Dev Team's servers experience bottlenecks. The update also comes through Sparkle if you select PwnageTool > Check for Updates... from the applications menu.
Wherever you get PwnageTool please verify SHA1 sum. It should be a3faf5c074d5556a40ce4c7678a51995b5767073.
In Mac OS X open a Terminal and type:
/usr/bin/openssl sha1 <path to PwnageTool.tbz>
This will output the SHA1 sum to your terminal window.
As always: Use on your own risk.
Latest News:
I've received feedback that the 2.0.3.1 update has not resolved the permission issues for some folks out there. I cannot personally confirm the reports as it seems to have worked for me. I'm following up with my readers tomorrow and constantly update this post for more.
I cannot confirm that there still is a problem with PwnageTool 2.0.3.1. I've tested it with my first generation iPhone and with my development device (3G). Both devices work like a charm and there are no permission problems anymore. Note: Unfortunately PwnageTool 2.0.3.1 in its About screen identifies itself as "2.0.3" only. Make 100% sure that you're actually using the updated version. May be it's best to pick the tbz archive via the direct link and open it right away. Otherwise in case something goes wrong while receiving the update through Sparkle you might not even notice using an old version...