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Did you test if the uninstall really worked? E.g. by trying to install a hack, e.g. launchpad? This is expected to fail for the case the jailbreak was properly uninstalled.
I had a similar problem once, but I didn't wrote what it was (I could fix this myself). But I think I had an old version of the jailbreak (I think it was yours, NiLuJe) installed and I took a newer version of the uninstaller (since I hadn't made a backup of an old one back then). This shouldn't be a problem from the documentation. The newer uninstall should work for older versions, I remembered. But somehow it wasn't. I was easily able to tell because after doing the uninstall, the device was still jailbroken. My conclusion back then was that I probably messed up the install of the first jailbreak by jailbreaking twice or by going from 3.0.x to 3.1 firmware. But I honestly didn't remember. I could fix this myself by installing usbnetwork and hacking the jailbreak out myself. But I would NOT advise this to someone who does not know exactly what each command entered does.
Root file system access (like via usbnetwork, alternatively e.g. myts) will allow more specific diagnosis.
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