Okay. Is it possible that you're affected by addiction or a status effect? Addiction to Buffout causes ST -2, EN -2, AG -3. Check the colors of your stats. Green is Base Value. Blue is Increased Value. And Red is Decreased Value. Without Armor, is the 4 ST colored in red? If so, you have to wait for the status effect to wear off for your stats to return to normal.
If that doesn't work. Then I'm sorry but it may be bug-related. Is your Fallout unpatched? I was looking through my files and one of the fixes of the patched version are:
The Doctor (Lori): * Makes strength improvement operation correctly even if the player wears armor
Unfortunately, I don't know what the specific problem was. But that's the closest thing I could find that could be related to your problem.
Sorry, if I'm grasping at straws here man. I've honestly never encountered that before.
For what it's worth, here are links to some patches that will eliminate virtually every bug in the game. Install 1.2 before 1.3.4 and read the readmes for installation instructions and compatibility issues.
http://www.nma-fallout.com/forum/dload.php?action=file&file_id=1076 by TeamX
http://www.nma-fallout.com/forum/dload.php?action=file&file_id=1075 (needs semi-official 1.2 patch) by TeamX
I think it was
The Doctor (Lori): * Makes strength improvement operation correctly even if the player wears armor
which patch fixed that ? 1.1 or 1.2 or 1.3
EDIT, I found a save, a in march the year before, and before I had the operation, but before I did everything else.