CAUSE FOR IMMEDIATE CONCERN - MACHINE NOT SHUTTING DOWN AFTER USE

Hello..
Usually I post very little with regards to my MDD G4, but it seems I am now suffering from some problems which maybe horrifying. Synopis of problem: I always run cocktail each night before I goto sleep and the computer goes to sleep.. problem: WHEN I ever have to reboot the system, it takes a VERY LONG TIME for the desktop screen to splash to the BLUE screen and reboot the machine.. WHAT IS GOING ON HERE??? Can someone help?? Is my hardrive dying or something?? Also, even with the large 120MM fan I have mounted in my system, it seems like its not doing its job and I can still hear trememdous amount of noise from my machine.
There problems never happened to me before, but I think its time for me to move to either an INTEL mac or POWER MAC G5. I think the MDD is dying!
Someone please help!

Japan,
Yeah, u could say I run cocktail pretty much everynight. So you r telling me not to run it everynight? I currently have 90-95GB space on my hard drive though. My OS install disk is Tiger 10.4 and I am running 10.4.11 - does it matter if it is 10.4?
Give me an example of corrupt directory.. All its doing is when I get ready to shutdown or restart to refresh the machine, it takes a long time before the desktop screen turns to the BLUE SCREEN and either restarts or shutsdown, depending what I want the machine to do. It never used to do this..
Also, I have three fans in my system.. As you know, I just recently installed a 120MM(large fan!) which is mounted on the roof of the optical drives. Though not really securly mounted I noticed the fan against the powersupply as its running.
Bottom front area where the ATA-66 drive cage is another small fan.. should I just remove that one since I have a very powerful 120MM fan cooling the case? last but not least, the PCI Fan card which is sucking out the hot air..
But I have noticed recently that my temperatures are RISING!! I am not sure if this means my machine is coming to its end, or is it that I just mounted the fan wrong on my optical drives' roof?
You also mentioned to me about defraging a hard drive where its not really needed in mac os 10.
Also, one more question.. is there a way to run OS 9.2.2 through sheepshaver on a Powermac based mac? I checked their website and it only mentioned non power mac based machines(intels).

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