Lightroom :: (Read-Only) Is Applied To 44k Photos While Using LR5 - Can't Save Work

Using MacPro (5 years old), OS Lion, full RAM, 4 HD's with 2 TB+ drives, plenty ofroom left over in all.
 
ALL 44k images located in one LR3 catalog (recent upgrade to LR5 hoping for remedy 2 days ago) show 'read-only' notice, so after doing any kind of work on them in develop, etc. I select all (in specific folder, not 44k photos!) then save it, a notice comes up and says these are 'read-only' files. Thus not able to save any work that is apparent in LR.  BUT, when exported as JPG all changes are saved.
 
I have opened various folders, NOT via LR, but via Finder (OS Lion) and opened one by one using PS 4 and they open fine in RAW converter window.  Save as PSD, all files look fine.  Same for JPG's.
 
The issue is LR, or hard drive or something along the chain where the photos, when viewed in LR, say they are 'read-only'.
 
Via Finder window I have opened various files (denoting read-only notice) and right-clicked to 'get info' on that specific photo. ALL files are 'read and write', there are NO files that are denoted read-only when getting the info.  I checked 50+ photos in 25 different folder locations.
 
Laptop test:
 
I started a new LR catalog in LR5, with ZERO photos and imported a few folders, with images that had 'read-only' notice to make sure I tested the same photos that had given me the read-only notice.
 
Did a test on photos with 'read-only' files on a laptop (OS Mountain Lion), pulled files from HD where ALL 44k photos are located.  Copied to thumb drive, imported with LR5, copied to desktop in test folder, all photos came in fine, slected all, did global edit to all images, saved all, all images were saved with NO 'read-only' notice.  This is true for a series of folders.
 
So my test, if it proves anything, is that either LR is messed-up or the HD is messed-up on MacPro tower or something is telling LR to show the 'read-only' notice to pop up.
 
Back-ups:
 
Back-ups were done from HD where all 44K photos reside, to 2 (two) other drives, within MacPro tower.  So ALL 44k photos are essentially the same.  This was a drag-n-drop not using Super Duper or similar byte-verification software.
 
why ALL 44k images say 'read-only', when viewed in LR5 in MacPro tower but NOT in laptop?  HD is 5 years old...could this be the weak link?
 
Also, considering to wipe the complete system drive (not HD where photos reside) and re-load everything from scratch to begin anew.  My concern is will this work and then, will wiping all drives and re-loading all images, then re-loading LR5 catalog will solve this.  I am resigned to a week of doing this if it works as right now, I am at a stand still and cannot go forward or backward.