I have only two logical explanations to this. One is that your server timezone and WordPress timezone might be different. Or the other reason might be that your MySQL server is very underpowered and it might have taken it a while to complete the execution.
Again these are just speculations and even I am not sure what really happened 🙂 But I am glad that your issue is fixed now.
In case you face this issue again do let me know and I will have a deeper look into it.