Command S works inconsistently and displays no warning dialogue box when closing

I am having a very strange issue with Photoshop CS6 - OSX 10.7 and 10.8 (recently upgraded).
I havent been able to figure out how to reproduce this bug though it happens all the time every day while i work.
I work on a file maybe for 10 minutes to 1 hour and when I save a file with command s photoshop does nothing. it will not save until i make any change that registers in the history and then it does save.
Even weirder photohop will close the file as though it had been saved giving no warning box with the "file has been changed, would you like to save?" message.
This has lead to me constantly saving things and double checking if files are saved, it has also lead to me missing a file from time to time and having to redo hour of work. This is a huge and odd issue for me.
The issue started happening when I recently reformatted and reinstalled all my software.
Has anyone ever encountered this issue? Do i have some strange combo of settings on that make this happen? I am at a loss and maybe a little blind to the real issue.
Thanks

any chance maybe Photoshop was in the middle of an auto-save when you initated the save. Have you tried leaving it alone for a while after pressing command-S and see if it ultimately saves?
I don't know whether an auto-save can get in the way of a real save - maybe not. In my case I've never seen what you're describing, and I have auto-save set for every 5 minutes.
-Noel

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