The reg permissions repair hasnt changed at all since v1.9.10
There are over a million keys that have to be gone through. And the exe that is setting the permissions needs as much cpu as possible. The fast the machine the faster the repair.
But if the machine is slower and you have other things using the cpu it will slow it down.
An example, ran all the repairs on a new machine total time was 15 min.
Ran it on a older machine with 2 core cpu took 40 min.
Then I had a 8 year old xp laptop, 1 core cpu and the system itself was so slow you where lucky to open even firefox in under 3 min. The repairs took 4 hours.
The CPU plays a big part as there is a lot of work to be done.
Shane