/System/Library/Extensions and /Extra/Extensions both have their own caches. Wherever you install the next is where you have to update the caches, so if you install a kext in /System/Library/Extensions you must update the caches in /System/Library/Extensions but you don't have to worry about /Extra/Extensions, and vice versa.
You can download and run Kext Utility to update the caches for both /System/Library/Extensions and /Extra/Extensions for any system 10.5 Leopard or higher. This utility is easiest for newbies, but it can be inconsistent and occasionally not update the caches properly, particularly on 10.7 Lion systems.
Depends on which folder you update:
Run the following command in the Terminal:
sudo kextcache -v 1 -a i386 -a x86_64 -m /Extra/Extensions.mkext /Extra/Extensions
This depends on your system:
10.4 Tiger/10.5 Leopard
Simply go to /System/Library and delete the files Extensions.mkext and Extensions.kextcache.
10.6 Snow Leopard
This is the same as updating /Extra/Extensions, but with the correct directory.
sudo kextcache -v 1 -a i386 -a x86_64 -m /System/Library/Caches/com.apple.kext.caches/Startup/Extensions.mkext /System/Library/Extensions
Enter the following in the Terminal: either
sudo kextcache -system-prelinked-kernel sudo kextcache -system-cachesor
sudo touch /System/Library/Extensions
Note that on 10.7 Lion systems, the kext cache by default is ignored. This will cause a slow boot process; to fix this you must boot with UseKernelCache=Yes, but no kexts in /Extra/Extensions will be loaded. For more information, see this FAQ.