I'm pretty sure Tobi did cancel Kakashi's Kamui, let me explain..
page 12.
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page 13.
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On the 12th page we see Kakashi aiming at Gedo Mazo. Immediately Tobi notices but he also has to dodge Naruto's attack. He does this by throwing his Gunbai and pulling the chain. Why does he do this when he can just go intangible. Because he needs his Gunbai to make contact with Gedo Mazo so he can turn him intangible and cancel Kakashi's Kamui! Notice on the 13th page the sound effect on the chain when Tobi says "to optimistic" to Kakashi. I think it means the chain had a certain purpose..
It's a possibility, but sadly we were given no explanation. Hopefully in the next chapter we'll be told how/why that happened.
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To add another point to my "kamui is instant" theory, I'm looking at the Kakashi vs Sasuke fight again.
As I went over in my original post, he was ready to take out Tobi with kamui. I explained that Kakashi now knows that it's possible to avoid kamui(which Deidara did, for the most part) if given enough time. Kakashi knows that Tobi can become intangible, and that if kamui is not instant, Tobi can easily get out of it, by simply becoming intangible.
Now, that alone may not be enough evidence for some people, as they may say "well, Kakashi may not think him being intangible would nullify kamui". However, another aspect plays in to this..and that's Naruto and Sakura.
What is one thing that Kakashi has done the entire series?
It's risk his life for his teammates and konoha. He'll die before he allows a comrade of his to do so(the quote from the manga in my sig tells you that by itself), so let's look at the scenario. He uses kamui, but Tobi reacts and becomes intangible because kamui is not instant. What happens then?
That leaves Naruto and Sakura vs 2 Akatsuki members and (albeit beaten up) Sasuke. Everything he's done in the past, including risking his life, and even dying over saving people like Ino, Shika and Chouji, who he has no real emotional connection to, tells us he would NEVER leave Naruto and Sakura to fight who he believes is Madara Uchiha, another akatsuki member(Zetsu, who he knows nothing about, so he couldn't judge his skill level) and Sasuke by themselves.
You also at that point HAVE to factor in the fact that he knows Tobi/Madara wants the kyuubi, so not only is he putting his students lives at stake, the people he vowed to never let die, he's putting the entire world at stake.
This really drives home the fact that he can make kamui instant, if need be, IMO.