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Also may be possible that

 Spoiler

Madoka actually gets more and more powerful with each recursion. First time, she died after the battle. Second time she was hurt, but just became a witch after. Third time she and Homura fight together and both get mortally wounded. Fourth time Madoka is able to take on Waluigi all by herself, and with just one blow as well. It's possible that she's more and more powerful, but of course we don't have enough information to really see if she's getting stronger or not. We never actually see the fights, nor do we see what becomes of Madoka after the fourth loop, aside from obviously becoming a witch. We know she took it out in one shot, but we don't know how. She probably used one of those FINAL BUSTER moves like Kyouko and drained her soul gem.


As for the thoughts on Kyubey, I'd say it's possible that there's just a bunch of contractors. Kyubey knew he didn't make a contract with her, but perhaps someone else did. He did find her suspicious in some way though. In our current loop, we saw that he even formulated a plan against her from the very start. If you notice, when she kills the first Kyubey in the hallway, a second one noisily appears behind her, and just waits for her to acknowledge he's there before running so that Madoka can see Homura as someone bullying an innocent creature and distrust her.

Kyubey never tells us his thoughts really. It would seem he knew something was up with Homura, but didn't think it'd be too important to look into. At the end of the fourth loop when he's all like "lol not my problem to deal with, everything's cool on my end" he doesn't really put the pieces together until Homura Time Roulette's the hell out of there.

He probably didn't try getting energy from her in this time line because he was planning all along to use Madoka anyway. He probably knew Homura would never be able to handle it on her own, so just let things progress as normal.

 Madoka Magica

You know, that might actually be the case. It also seems like Madoka retains some vague memories from the previous recursion as well. Seeing as in the first episode she had a dream about Homura's solo run through with the Walpargeist Night (spelling?). She also seemed to have some sort of recollection about Homura when she stepped in and stopped Kyubey from making a contract with her back in episode 8.
I think that the fact that the wish made determined the nature of the girls' powers may have something to do with this also. Since Homura's wish was to go back "to protect Madoka," her power may in fact bring Madoka's memories and strength back in time as well; thus resulting in Madoka becoming stronger, as well as her semi recollection of the previous loops.