Q: Permissions never get repaired

Mac OS X: Disk Utility's Repair Disk Permissions messages that you can safely ignore

A HDD noise that is periodic may indicate an impending failure. It is unrelated to file permissions. Back up your important information if you have not already done so, then boot OS X Recovery and run Disk Utility. Describe any errors it reports in red.

1. http://support.apple.com/kb/TS1448

You might also try booting in Safe Mode (hold Shift key right after pressing power button, until you hear startup sound). Once you get to desktop, open Terminal (~/Utilities/Terminal) and type:

sudo diskutil repairPermissions /

2. Why do you assume the disk activity has to do with permissions? Try ~/Utilities/Activity Monitor, and see which processes are running. If you decide to quit any processes, read this first: http://support.apple.com/kb/PH5147

Yeah, what John Galt said.

Secondly, I always hear my hdd disk working in the background, you know kind of these mild clicks every two seconds like its trying to write or read something from the disk...

I have a perfectly good, new external drive that's like that. Some drives are just noisier than others. Depending on what you're actually hearing--and I have no way of knowing that--could be a drive with a problem, or something you can comletely ignore.

The noise that's really bad is called the "click of death," and I don't think it sounds like the drive is reading/writing normally.

Normal sounds include:

 

    Whining noise during drive spin-up.

    Regular clicking or tapping sounds during drive access.

    Hard clicks when the drive heads park during power saving modes like Standby or Hibernation.

http://knowledge.seagate.com/articles/en_US/FAQ/174571en

Also

http://www.datacent.com/hard_drive_sounds.php