If I restore using Time Machine, will I restore permissions also?

Here is the deal. We have a MacPro and I would like to use Time Machine to backup the computer, then wipe the hard drive and the restore only the software and media. What we DO NOT WANT is for any of the problems (like the permissions that are messed up) to be restored also. When  I say permissions I mean in our office  we have to hold shift to start up in safe mode, then restart, plus other stuff . I really don't want to get into all that. Please tell me if problems will be restored as well, after the use of Time Machine, cause that's what we want to avoid.
Speak slowly and clearly please.
MacPro Version 10.6.8
2 x 2.26 GHz Quad-Core Intel Xeon
8 GB 1066 MHz DDR3
I'm not sure of the year (let me know if it matters in this case)

Is there anyway to avoid that.
No.
How can I, "exclude from the backup?"
Apple menu > System Preferences > Time Machine > Options...
So using Time Machine, in my case, is a waste of time?
Not necessarily. You could restore from a snapshot taken before the damage was done. In that case, you lose all more recent changes to your files, but you could restore those selectively.
Also would upgrading to Mountain Lion solve this issue?
I'm not sure what the issue is, so I don't know.
Is the way to restore the OS to default, but leave all new media and new software in place?
Boot into Recovery (command-R at startup) and select Reinstall OS X. Don't expect that action to solve any problem other than corrupt or missing system files, which are relatively rare.

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