The directory /boot/var, which contains system log and temp files among other things, is hidden from the Tracker to discourage normal usage (although it is visible from File panels, so you can quickly open up log files in text editors when necessary).
If you do want to see the contents of /boot/var in the Tracker, just open a Terminal and type:

/system/Tracker /var &

(/var is a symlink to /boot/var).