I don't think we know for sure yet. Elistia is correct that the Doctor's enemies accused him of creating it. My question, how real were the enemies. The Romans were fake and we know both the Romans and the Pandora were taken from Amy's memory. Why couldn't the enemies be taken from her memory also. I still think that episode left more questions than answers.
If I remember correctly, it's not the Doctor who causes the cracks, it's the TARDIS exploding that does. All his enemies thought it was him and tried to trap him forever in the Pandorica, because he--they thought--was the only one who can fly the TARDIS.
That's a good question ! maybe it's because of The regeneration ten/eleven and the TARDIS crash . maybe ( that's what I thought first) it's because of all the parallel universe that have been open and closed, and especially when The Time Lord and all Gallifrey children try to come on eart in The End Of Time movie .