I always got the impression that Obi-Wan *suspected* it was the same guy but wasn't sure until Jango started to be evasive with his questions. I watched the film last night and there is a moment where Obi-Wan visibly leans to his left to look over Jango's shoulder at the armor, but Jango actually moves out of the way to give Obi-Wan a better look before telling Boba to shut the door. Odd.
That said, another thing I noticed (or didn't notice, as the case may be) was that the shot of Jango flying off into the sky after he "darts" Zam in the alley is very quick and very blurry. All I can make out personally is an indistinct blob with rocket trails moving up. Even with Jedi powers, I doubt Obi-Wan's eyesight is good enough to make out more than a silver and blue blur flying away at night.
So, I guess where I'm going with this is to agree with P'dubs. Obi-Wan wasn't sure but put two and two together after Jango started answering questions with cryptic answers. The armor only helped him come to that conclusion, I suppose.
My main question (and one that Ben Burtt actually does bring up in the commentary track) is where Obi-Wan was supposed to put Jango on the way back to Coruscant had he captured him. I guess he'd just put a gasmask on him and strap him to the hood of the Jedi Starfighter or something.