Ah, okay, well you ended up with Security Warning due to a non 100% stock ROM, and tampered due to a non 100% stock recovery.
the ruu will put your phone back to 100% stock (and also wipe it in the process), and then it's safe to go from S-Off to S-On.
One thing worth noting, is that even on 100% stock everything, going from S-Off to S-On on hboot 1.55+ (ie base 3.xx+) will likely trigger a "tamper detected - rebooting" and TAMPERED is back in bootloader.
i cannot confirm this to be a certainty, some people have been able to go s-off to s-on without it happening, and some not.... so my guide goes by the thought: why risk it?? just do it on hboot 1.44 (1.xx base) or 1.54 (2.xx base).
I'm planning on doing it on Hboot 1.44 as well