Extreme permsions problem - desperate please help!!!

I have repaired permissions three times, run tech tools twice, deleted preferences etc and it is not fixing the problem - which has got to be a permissions problem- here is what happens:
1. In illustrator CS:- when you have a file open and you have made changes but want to close it with out saving the changes - it wont let me close the file or quit illustrator util I have sved the file. no errors come up it just ignores me! I have to force quit out of it to close illustrator....unless I save the changes!!!
Also in illustrator I can't change any of the print settings - it will only stay on default, again the buttons won't respond
2. When I do get info on a folder I can change the settings (unlock etc) on a file but it won't apply to enclosed folders - whenn I click the buttin it does nothing!
3. Sometimes I can't save files into certain folders - it won't let me!
4. when saving it sometimes says there start up disk is full when there is 100G on it-I have to saveit to somewhere else then copy it over
5. in photoshop CS I can't save ontop of another file I have to save into another file then delete the old and put the new file in its place
Think thats about it
I have a G5 1.8ghz 10.3.9 with an external hard drive with three partitions and another extra internal hard drive
The external hard drive has just recently been reformatted
All the items seemed to be related as they all started happening at the same time about the when the external was reformated
please help I feel I have tried everything under the austrailian sun!!!!

I have repaired permissions three times, run tech tools twice, deleted preferences etc and it is not fixing the problem - which has got to be a permissions problem- here is what happens:
1. In illustrator CS:- when you have a file open and you have made changes but want to close it with out saving the changes - it wont let me close the file or quit illustrator util I have sved the file. no errors come up it just ignores me! I have to force quit out of it to close illustrator....unless I save the changes!!!
Also in illustrator I can't change any of the print settings - it will only stay on default, again the buttons won't respond
This is not a permissions problem. More than likely it's a problem with Illustrator, one of its preference files, or your hard drive, or your OS is corrupted.
2. When I do get info on a folder I can change the settings (unlock etc) on a file but it won't apply to enclosed folders - whenn I click the buttin it does nothing!
This is a bug in 10.3.x. Upgrade to Tiger or use the freeware utility BatChMod (www.versiontracker.com.)
3. Sometimes I can't save files into certain folders - it won't let me!
This may be a permissions problem related to the specific folders. Note that some folders may have permissions set to deny access for a reason. Be sure you are not trying to access folders you are not supposed to access. BTW, repairing permissions will not fix this. Repairing permissions with Disk Utility does not affect the permissions on folders belonging to the user.
4. when saving it sometimes says there start up disk is full when there is 100G on it-I have to saveit to somewhere else then copy it over
Pretty good sign your hard drive needs repair. Again, this has nothing to do with permissions.
5. in photoshop CS I can't save ontop of another file I have to save into another file then delete the old and put the new file in its place
This may be the way PS works or you may be trying to save over a file in use. Some apps want you to use Save As to avoid overwriting another file.
Off hand I would say your hard drive is in dire need of repair. It's also possible your operating system has become seriously corrupted and possibly even some of your applications. To start the process to normal first do the following:
Boot from your OS X Installer. Be sure to use the installer for the version of OS X you have installed. After the installer loads select Disk Utility from the Installer menu (or Utilities menu if using Tiger.) After DU loads select your OS X volume from the list on the left, click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. Now select the hard drive entry (this is the one with the Mfgr.'s ID and drive size) and check the SMART status in DU's status bar. If it does not say "Verified", then the drive is failing. If no errors are reported, then quit DU and return to the installer. Now shutdown the computer for a couple of minutes and then restart normally.
If DU reports errors it cannot fix, then you will need Disk Warrior (3.0.3 for Tiger) and/or TechTool Pro (4.1.1 for Tiger) to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.
If this does not fix the situation, then you may need to reinstall OS X. If these problems have been around for a while, then you have been updating Tiger on a corrupted drive or system. If that be the case then reinstalling is the only solution that is guaranteed to return things to normal. You can reinstall without erasing the drive by doing an Archive and Install. However, do not attempt an Archive and Install unless the hard drive has been verified as OK.

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