All files are locked, a new entry in permissions and more

Following instructions from here on how to try to correct another issue, I was repair permissions and to boot in safe mode. Since then all kinds of things are messed up.

I had to reset PRAM because the home and boot screens were were all stretched out of whack (this situation has occured once before shortly after getting this new machine)

EVERY SINGLE DATA FILE created prior to this safe mode is now LOCKED. EVERY ONE!!!!!! If I try to save any file so far I have tested, I am told the file is locked and I do not have permissions. My user mode didn't have administrative control before, but I changed that because unlocking everything to use it was more complicated having to enter the username and password. New files created are also locked. However, a new Pages file I have tested shows locked but it will save to the same file with a CMD-S.

Having to unlock files to save work in them really slows work. Apple not allowing Save As on Apple apps is getting really tedious. I tried with a non-Apple app (PhotoShop) and its files are locked after creation. This means I have to unlock every stupid file before I can save it, then it relocks If I go into Get Info to unlock the file, as soon as i close that window, the file shows locked when I do a new Get Info. This is not a good user experience!!!!!!!!!!!!!! I have hundreds of thousands of files used in publishing, graphics, photos, and music. I tried to save an existing Photoshop file back to the Desktop and was told I could not save because was locked - that I needed to unlock the file or enclosing folders. When Photoshop closes it says can't save Preferences because file is locked.

If I unlock the Sartup drive it relocks as soon as the Get Info window closes.

In Sharing and Permissions the user called Everyone has a custom settings and some files even have two Everyone entries. Newly created files have had the User with Read & Write and Staff and Everyone with Read Only. My user folder Get Info shows locked with the user, staff and everyone with Read & Write permmissions. If I unlock in Get Info it reverts to locked after I close the Info window.

Safari opens to the same page on this forum where another problem was discussed. I have reset selected items in Safari that I thought might have caused this, but no change.

Pages keeps opening a page that was thrown in the trash and is not even on the computer (at least doesn't show in the finder),

Numbers keeps opening a file that was opened and saved days ago.

iDVD will open the same project each time, even if something else has been worked on since.

I have cleared recent entries in these programs and the field keeps coming back when I open again.

I unchecked the Restore windows when quitting option in General Sys Prefs and when I open it again it is checked. I know that Lion will reopen a page if I quit without closing the window first. Now, at least with Apple apps, the same file opens now whether it exists or not as well as the new file I am opening by clicking on it.

I have run permissions check in Disk Utility several times.

It seems that it is affecting Apple apps that remember where there were last and the visiting history.

Autosave on apps other than Apple can't save because the files are locked and I get error messages.

iPhoto files saved on a firewire drive are also show locked but testing on a duplicate file, I found I can edit with PhotoShop and it will save the changes.

With Finale, it has saved the files, even though locked. The odd thing is that in the finder it shows the correct creation and modifided dates, but it shows an old last opened date. Pages documents show all three with correct dates/times.

I suspect there is at least one if not more Pref plist files that needs to be fixed, but I have now idea where to start.