We are assaulted to the point of irritation with the idea that Tony is a cosmic genius, yet he makes absolutely no effort to pay any attention to what is happening with his company. And don't say he was a hands-off inventor who didn't really get involved with the business side of things -- after three months of being held hostage by cave terrorists, the first thing he does is completely restructure the business by dissolving the weapons manufacturing arm. It's incredibly important to him, and therefore baffling that he wouldn't check in from time to time to see how everything was progressing in the wake of his job-destroying mental breakdown.
But he's too busy screaming at robots in his basement and zipping around Ferris wheels in his rocket suit to be bothered with any of that bullshit. If Tony had decided to check out the proceedings, he would've noticed that Obadiah was trying to lock him out, which in turn might have prompted him to take a closer look at what his partner had been up to for the past several months, thus uncovering Obadiah's nefarious plot (which, to be fair, seems to change on a scene-by-scene basis). But Tony, the business-savvy super genius who could've hacked any secret file on Obadiah's computer with a sidelong glance, didn't think to make even a cursory checkup on something that was surely big enough news to hit the front page of The Wall Street Journal.