Haha, I read that at the time and thought it was interesting, and it completely didn't occur to me to ask that question
Anyway, I think that basically the answer is that the Chinese government's commitment to attracting big Western companies into China outweighs their desire to enforce their anti-union legislation. Reebok has (I believe) a universal code of conduct that states that anyone affiliated with it must respect the right of workers to bargain collectively, so had the government investigated them and taken action regarding the ballot it would have effectively barred Reebok and most likely several other big companies (Levi's is another one that has the same rules) from importing from China.
Plus, the factories, whilst producing Reebok goods, were actually owned by investors from Taiwan- and that's another group of people that the Chinese government doesn't want to scare off.
Finally, I think they managed to make the unions independent- in that workers were allowed to elect who would lead them- they allowed the official Chinese trade union confederation (controlled by the govt.) to monitor them, and they then accepted it as an affiliate member once the union had been set up. The book I got this from was written in 2003, and I haven't found information on it anywhere else yet, so at the moment I can't say whether this affiliation with the official union confederation has stopped the Reebok union functioning properly over the last four years, but I guess it's probably quite likely that it has interfered quite a lot.