I haven't seen shutdown invoked as you do before - I always thought that a flag like -h had to be there as well; shutdown -h now for halting. To reboot, change the -h to -r.
But still; you should check that the apm module is loaded. Look in /etc/rc.d/rc.modules and search for apm. If the line is commented, uncomment it - now apm will be started when you boot up your computer. Also, if the line was commented, then apm is not loaded currently. Do a modprobe apm and it will be started. Now you can halt your computer to see that it works properly.
I find it a bit strange that a file systems check is necessary after the system is shut down, even though your computer doesn't switch off. Do you wait to press the power button until it says "Power down."?
Another thing about the file checking. I guess you aren't using a journaling file system? And in that case I assume you're using ext2? To get rid of those tiresome FS checks, you can convert your file system from ext2 to ext3, using tune2fs. Make sure the partition you want to convert is unmounted (if necessary using a boot/rescue disk or a live CD like Knoppix), for instance /dev/hda3, and issue tune2fs -j /dev/hda3. The conversion from an ext2 to an ext3 system should not do any harm to your data.
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