[[ So, I cannot 'move' hundreds of gb of data every often, because of apple's fault. Disk utility seems unable to fix permissions after this 'disk corruption'.
I need an alternative way, faster, leave my disk 'as is', and fix permissions. ]]
If you indeed wish to "fix" the problems that Disk Utility is reporting, than I don't believe you have a choice in the matter.
You should:
1. Copy all the data on the problem drive to a DIFFERENT drive
2. Re-initialize the problem drive with Disk Utility
3. TEST the problem drive with DU - run the "repair disk" function about 5-6 times, make sure it comes up clean each time.
4. RE-copy your data BACK TO the drive from the backup you used.
If you DO NOT want to do this, I suggest you get used to living with the permissions problems you have now...