As of 10.7.0 Lion, the kextcache mechanism has been changed and the old mechanism of using the "Extensions.mkext" file is now legacy. The new default system is now using kernelcache,which is in the same location as the previous .mkext file (/System/Library/Caches/com.apple.kext.caches/Startup).
The slow boot up of the system is due to Chameleon not using these caches (UseKernelCache=No by default) but loading the extensions one by one thus taking much longer (but in this way, loading the extensions both from /Extra/Extensions AND /System/Library/Extensions and is in effect,like booting with the -f bootflag).
A fast boot up is achieved by using the boot flag UseKernelCache=Yes but take note, this way, all of your additional kexts must reside in /System/Library/Extensions since /Extra/Extensions is ignored.
How to force rebuild the kernel cache is covered here in the 10.7 Lion section.