I've pointed out the issue to Flatlander,he said it was because of the new timeflow commands.
Eventually , setting a cap on the framerate to 34 fixed it I think
You could also use the entity animation speed command to make them slower, but that had some issues.
Your last option is the timeflow=x command to be lower than the usual 100, but then you'd have to change a lot of commands to perform faster.
PC Specs:Windows 7 Ultimate 64-bit,Intel Core i7 960 @ 3.20GHz,NVIDIA GeForce GTX 480,12GB RAM,2x Western Digital 997GB HDD