Another thing you might want to check on your missing apps...
Could it be that you've still got disk images on your desktop, but since they're no longer mounted after your reboots, you're not seeing what you expect?
If this is the case, try opening he disk images (file that end in .dmg) and see if what you expect to have been there. Once you see an application in the disk image, cmd-c, then cmd-shift-a to open applications, then cmd-v to copy the app in.
