Using MM to do updates is only required if you have an older CFW. I don't remember off hand when they last changed the keys but I know it is not required for Rebug 4.46. MM looks to see it there are older firmware updates and grabs those I believe.

I always let games update by themselves as a first attempt as this almost all ways works. In the case of GT6 I install six different regions and since I only have a 150 Gb drive in it I go through a complete install for five of those every update and every time i just let it update normally and never have a problem. I think the problem arises from using MM or manually installing the packages.

For the next update I backed up the internal data before deleting it so I can test if simply restoring it will be faster.

Of course I could just be overwhelming lucky with installing so many times.