Computer will only (sometimes) boots after CMOS reset

[#1]

I changed the PSU on my computer after the last one started making some strange noises (computer was still running ok though), however when I switched it on I just got a cycle of all the fans coming on, then the DVD drives spinning then clunking (and repeating that over and over again). Someone suggested that it was getting stuck in the boot cycle (it wouldn't post), so I reset the cmos by using the jumper and voila! the thing started to post.
It went into the bios settings, I setup the hard disks to boot in order, then saved, exited and then got one of 3 outcomes:
The PC booted into Vista
The post screen said "Chassis Intrusion" (even with the side on)
The PC went into the original cycle (DVD drive spin and clunk).
The PC was off for about 5 months and some forums suggest the battery could be dead/dying and causing weird behaviours, others have suggested this isn't the case.
The PSU was swapped like for like (500W) and is plenty for the current system (I'm using it to write this post!). The motherboard is an Asus A8R-MVP. Suggestions?

[#2]

Have you tried booting from CD?
Have you checked that you didn't disturb any internal connections during the install?
Whilst the PC was off for 5 months was it also disconnected from the mains?
Usual signs of battery failure are losing of BIOS settings - especially date/time.

[#3]

I haven't tried booting from CD, but then the CD drive doesn't seem to work without resetting the CMOS because of the endless loop.
I checked the connections from the bottom up, they all seem ok.
The PC was disconnected from the mains.

[#4]

You can disable the Chassis Intrusion Detection with a jumper on the motherboard.
Not necessarily a source of your problem but one less thing to worry about.

[#5]

What happens if you unplug the power lead to the DVD drive?  Does this limit you to the first two of your possible outcomes or does the computer still fail to complete the POST (only less noisily)?

[#6]

Fails to complete post but without the noise. I've tried with just the GFX and HDD plugged in but still the same result. I'm using the computer now, but I reckon it'll take another few CMOS resets to get it started once I shut down again.

[#7]

The next step is to unplug all optical drives, hard drives and any peripheral except the mouse and keyboard.  In this state the computer will only be able to complete the POST and then stop (because there is nothing to boot from) but if it still plays up the problem comes down to one of your motherboard, your CPU and the RAM memory.
The next step would be to unplug and reseat the RAM.  If you have more than one module, try them one at a time.   

[#8]

I have tried unplugging everything except the HDD and it refused to post, will try that too. I have removed and reseated the RAM already with no luck. I'm almost convinced it's the CMOS or the CMOS battery that's messed up. When I did manage to get the computer to boot last night it was perfectly fine for the few hours I used it, then failed to boot again when I tried to restart Vista.
The only other oddity I've seen is that the primary master HDD is actually being identified as the tertiary master (it's a SATA disk and I am on the SATA 1 controller. I've tried the other SATA controllers with no luck), meaning I have to select it as the boot disk as otherwise the BIOS defaults to trying to boot from one of the slaves (which would work as that has XP on it).
I'm going to see if I can get another CMOS battery at the weekend, otherwise it'll be a new mobo, processor, RAM and fan!