InDesign CS6 (Mac) will not package fonts

I have hundreds of fonts on my machine and have never had any issues with packaging fonts until CS6. CS5.5 works great, even today with the same files that will not package in CS5.5. However, I cannot use 5.5 due to the other 7 designers all using CS6. None of them are having issues - they are also all on PCs with me being the only Mac user.
"Cannot copy necessary fonts" is the error that I get when packaging anything that uses a font other than the default system fonts. Our primary font is Gotham, which we have 12 licenses for. Scala, also licensed, is another problem child. These all package fine in CS5.5.
Machine specs:
Macbook Pro
OSX 10.7.5
2.3 Ghz
16 GB memory
Fontbook is our font manager
I have tried Fontnuke, Font doctor, resetting permissions, deleting InDesign prefs, copying the fonts in question into my Applications font folder, basically any solution that I could find online has been tried with the same error message presented at every package attempt.
Any help would be seriously appreciated. Its embarrassing for the Sr. Art Director to be the only one on the team that cannot package correctly.
Thank you

I believe I have this problem, or very similar, in both CC and CS6. It happens on both machines I use, detailed below, when I convert from previous version InDesign files:
Machine #1, Mac Pro:
InDesign CS6 v8.0
Mac OS 10.8.5 (12F45)
3.06 GHz 6-Core Intel Xeon, 24GB RAM.
Machine #2, iMac:
InDesign CC v9.2.1
Mac OS 10.9.2 (13C64)
3.4 GHz Intel Core i7, 16GB RAM
Example:
1. I open a packaged inDesign file in InDesign CS6, converting it from the previous version (CS5 in this case, according to IDentify.jsx). The fonts are all working.
2. I resave the file as a CS6 file, fonts are all still working as long as I don't reopen the file. (However, if I close the file and reopen it, it will show fonts missing.)
3. I package the file from CS6, no font problems shown in packaging.
NOTE: I do not get a "could not copy fonts" error at all.
4. I open the new CS6 inDesign file inside the package folder. It will say "Fonts Missing: Calibri" or similar, showing some of the fonts missing, not all.
5. I can easily manually copy the fonts from the old package into the new package and fix the issue. The fonts are not damaged, missing, locked, or have any visibly different permissions from the other font files when I get info.
So for me the problem happens particularly with the resaving of files from older versions of InDesign, not necessarily with packaging them. If I open a CS5 file and resave as a CS6 file, then reopen that file, it typically has a few fonts missing. This happens to also effect packaging even though it will show all fonts present in the Package window and give no error message.
Checking the CS5 fonts package, it contains both a AdobeFnt14.lst and a AdobeFnt13.lst. Not sure if this pertains to the problem or not, searching these files reveals that both contain the "Calibri" font that went missing on CS6 conversion.
I have tried resaving and repackaging a CS6 file (not converting from CS5) with the same fonts that went missing in the conversion and they all were copied fine.
Obviously this is devastating if I package and send a folder out only to find out it secretly didn't have all the fonts!
I have tried "fix permissions" and "clear font caches" but this has no effect on the problem.

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