I kind of got that feeling too, but there wasn't much there to go on. I figured the big metel room had something to do with it...and why put in such a big window?
Maybe Eden shut down the power blocker when she walked in so she could use her powers on Sylar. She controlled him once, iIguess she had no reason to think she couldn't do it again. Of course, she surprised him the first time, so he didn't have time to resist, either.