on I have root, but S-on?

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Im in a rather odd predicament with my new thunderbolt.
I ran this set of instructions(http://forum.xda-developers.com/show....php?t=1011623), and everything went well, BUT i have s-on(huh?), and I cant get rom manager to work. I say rom manager wont work because it wont boot into the clock work recovery no mater how many times i hit "flash clock work recovery" at the top.

any way i can just turn s-off and get this rom manger working?

I made sure I tested if I had root by running root checker (busybox is also installed correctly according to it)

Ignore me Sorry. lol

So any help possible? Also.would re following the root instructions on top of an already rooted phone cause issues?

I would say flash the back to stock RUU and try again. Sounds like you missed a step in the process, and if you used an automated rooter, don't.