I have exactly the same problem. I had the IDE installed from two weeks ago and had no problem saving files in any subfolder as long as I renamed them. Yesterday, I had to remove and reinstall the IDE and Arduino folders to get SPI.h to work properly with the Sparkfun WiFly. So, new IDE downloaded Friday, Feb 8th
Now, in spite of renaming files I cannot save (changes) in any folder in the Libraries directory. I've used Get Info to make Libraries and all it contains Read and Write, but the message appears to be coming from the Arduino IDE. I've checked the IDE preferences.txt file and cannot find an entry that appears to hold the magic to unlock this issue.
I moved the folder containing my examples into the Arduino folder, the one directly above Libraries, and can now save changes to my programs. Everything else appear to be OK.
So, has some coder at Arduino decided we'd all be better off if we were unable to save changes to any file located below the Libraries folder? Was this change made in just the last day or two? Why was I able to save changes before? Is this a setting that I can gain control of?