same problem here. What if I just uninstall it?
I tried using the nVidia web drivers + CUDA 6 was getting Kernel Panics so I manually uninstalled CUDA (nVidia doesn't seem to have an uninstall script)
Here's how I removed it: (if you are like me and hate typing sudo over and over again, just su to root by tying
su at the command prompt and entering the root password. If no root password has been assigned you may get an error so you can type
sudo passwd root and enter a password of your choice. Then you can type
su and enter the root password you chose. The prompt will change from $ to #. Now you can do the procedure without always having to type sudo.
Do be careful when logged in as root though as it is the super user and there won't be any safety net if you make a mistake)
1. sudo kextunload /System/Library/Extensions/CUDA.kext
2. cd /Library/Frameworks/
3. sudo rm -rf CUDA.framework
4. cd /System/Library/Extensions/
5. sudo rm -rf CUDA.kext
6. cd /Library/LaunchAgents/
7. sudo rm -rf com.nvidia.CUDASoftwareUpdate.plist
8. cd /Library/PreferencePanes/
9. sudo rm -rf "CUDA Preferences.prefPane/"
10. cd /System/Library/StartupItems/
11. sudo rm -rf CUDA
12. cd /usr/local/
13. sudo rm -rf cuda
14. Reboot the system