The direct transit visa should apply for both cities, isn't it?

Hey,
I have a flight planned from Taipei via Shanghai to Beijing. In Beijing the flights of the first ticket end, I get my luggage, have to check in the second flight, going to Ulaanbaatar within 3hrs. If I see it correctly, I have to enter PR China twice (in Shanghai and Beijing), both times less than 4hrs. In total I have finally left PR China within 11hrs.
Thanks a lot!