Runner on first, ball hit to short, throw goes to second where the ball is bobbled, drops and rolls three feet away. Second baseman picks ball up with bare hand, rolls over and slaps second base with his glove before the runner gets there.

Any reason why this would not be a force out? The second baseman did have control of the ball in his bare hand.

Nope, no reason at all why that would not be a force out. In fact, it <b>is</b> a force out.