If you are trying to use the GUI version, may I suggest you do a restore of the iPad (through iTunes) and then try the Windows command line & CLI version as outlines here: Tutorial: Jailbreak the iPad2 on 5.0.1 with Absinthe Using Windows and the CLI Tool
It's worth a shot, yeah? Sometimes, Windows set-ups are so different for each person that I imagine the GUI gets a bit confused.
*Disclaimer: I did not use the GUI tool to do my jail break - so I cannot say what happens, nor do I really know anything on how it works.
Sorry, but other than that suggestion, it's all I've got.