Well, its somewhat difficult to diagnose the cause without being able to look over the actual computer but from the error description I would have to guess it is a write error to your hard drive. What I mean by that is, there appears to be something physiacally wrong with your hard disk that is preventing the updates from being written to the disk. Since it sounds like you were able to install FFXI on your system without any trouble I cant be certain of this since it should affect your abillity to install almost anything.
Something I recomend you do before any of the suggestions below is to run an error-check scan on your main HDD to see if it can detect any problems, if it can then you have a good idea that its the HDD but if it doesnt then keep in mind that you still cant rule out the HDD as being the cause.
Do you have any blank HDDs? If so I suggest that you make a clean windows install on it and load up all the appropriate drivers. Then install FFXI and see if it will update without problems. If it does then it is likely 1 of 2 causes, either your HDD has something phisically wrong with it like I described earlier or there is something wrong with your windows installation on your main drive that prevents the updates from being installed correctly.
The only way to differentiate between the two causes would be to backup and then wipe your current main HDD and do a clean reinstall to see if that fixes the problem, if it does then it was the windows install. If it doesnt then it is probably the HDD. I say probably because as i said earlier it is difficult to determine the exact cause without being able to get into the system, so I cant gaurantee that even the likely causes are the culprits, just keep that in mind if you decide to act on any of this.
Something you mentioned in your post makes me curious, you said this was a custom system... does that mean you built it yourself or that you had someone else build it to your specs?
Just a general warning, if you are getting into building your own systems and dont already know this, its important... always, always, always, have a backup system. Having a backup system is important not only in case you make a mistake with your main system that prevents you from using it but just to have somewhere to test theories on what might have gone wrong on your main system. I always keep my previous system around, just in case. This precaution has served me well and is something that i continually see not being done even though it is just basic common sense.
Ill post this here and on the post you made on the main forum so you will see it either way.
Good luck with getting things up and running. >^^<