Found a proposed solution for the problems in JB using blackra1n, you can try the steps...
You can try these solutions:
EDIT: instructions from
Cydia Updates That Matter Blog:
UPDATED: BlackRa1n stuck at the “Running…” Screen? Here’s the fix!
UPDATE: It seems some of this might need a little bit more detail and it also seems that some different Service Packs might respond differently. I have tested this on Windows XP (SP3) and Windows 7. Here are some more detailed instructions:
Step 0. Ensure that within iTunes you have unchecked “Sync Automatically” and under Edit -> Preferences, Devices, choose Prevent iTunes from syncing with Devices Automatically.
1. Ensure that your iPhone is on. You can see your Springboard. Plug your iPhone into your computer and ensure that iTunes recognizes it and preform a sync/backup/update.
2. Once you have completed this, close iTunes completely. Press the start button and choose Run. Press Ctrl+Alt+Del and check your task manager to ensure that any iTunes processes are closed, such as iPodService.exe, iTunesHelper.exe, etc. These must be turned off.
3. Ensure that your copy of blackra1n.exe is located in C:\blackra1n.exe.
4. Right click blackra1n.exe. If running Windows 7 choose properties, and then compatibility. Choose to run in Windows XP SP3 Mode.
5. Right Click blackra1n.exe and choose Run As. Chose the Administrator account and enter in the password.
6. Once blackra1n.exe is running, click Make it Ra1n.
7. You should see your iPhone automatically reboot and show a usb cable and iTunes, your typical restore/dfu screen.
8. You should see blackra1n.exe change to Running.. and GeoHotz face will appear on your iPhone. It will automatically reboot when done and that is when you should see the “Jailbreaking complete” dialog that likes to appear when you manually restart after no response.
Mod edit: Added the source of the article as well as newly added preliminary info updates by the author to the write-up. 
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