Major problem with rooting

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http://forum.xda-developers.com – Hello All, I followed the tutorial on how to root HTC One X with Hasoon2000's HTC One X All-In-One Toolkit. I encountered a little problem installing CWM, so I manually installed 5.8.4 (which works great). then I went on and did the root thing through the software. It all seems good - I got the SU file under System/xbin, and got Superuser app on my phone. But when I try to work with things that need root, it tells me that I don't have root permissions. Even downloaded Root Checker - and it also says I don't have any. now, when I try to install SuperSU from the recovery mod (HowTos)