Never ending busy mode; what is going on?

[caravel]

NB: I run a dual hard drive set up; primary for windows and core programs, secondary for games and frippery.

At the start of last week I was browsing the internet when my cursor turned into the 'busy' hourglass. Several minutes later it was still 'busy' and I still couldn't do anything like call up task manager, minimise my browser window, open the start menu, etc. I had to do a hard reboot. The PC then would not start up. It kept giving me an mesage about an "intel boot agent" right before the windows splash screen should have appeared. I turned the PC off, let it sit for a bit, turned it back on, and it behaved as though the hard drive didn't have windows present. I brought a new hard drive, replaced my old primary, installed windows and set the basics back up. The next day I connected up my old primary drive and recovered my important files from it. The PC was fine until today.

Yes it looks like the hard disk drive simply failed. The symptoms of the boot agent loading and the non responsiveness, hourglass etc all point to this being the case.

This morning I reconnected the secondary hard drive. Everything was ok; I wiped it and began to reinstall my games. Everything was fine until, after installing Sword of the Stars and its expansions, the PC went into busy mode again. It didn't end. Reboot required. Fortunately no damage appeared to have been done. Not longer after it went into busy mode again, and again I had to reset.

I mention Sword of the Stars by name because there's a bit of a theme and I don't want to leave out information which might help solve the problem. My PC had been running without a single issue for 2 years and 4 months, since the day I built it until several days after I first installed SotS. Then I got the busy mode which forced the new hard drive and reinstall. After the reinstall it was fine for a week, until SotS was installed.

It's probably not SotS fault but there's definitely something wrong.

The busy modes were prompted by:
1. Reading a favourite web page and doing nothing else (this is the one which required a reinstall)

2. Pressing the pause button on a download window whilst a game (SotS, coincidentally) installed. Both installer and downloader were running in tiny windows so I didn't need to minimise a window or anything at all in order to press that pause button.

3. Trying to move a single entry in my start menu while JKdefrag ran.

Virus scans come up clean.

Nothing unusual, and nothing I haven't done hundreds of times in the past without problems. I used to be able to do three or more things at once without the least hint of trouble or even slowdown.

PC specs:
Windows XP home
Intel E6600 Core2Duo
MSI Intel 975X PCI Express Motherboard
BFG GeForce 8800GTS 640MB
2GB Corsair DDR2 RAM
1 76GB raptor hard drive (my brand new primary)
1 160GB western digital caviar hard drive, about 2 1/2 years old. (the original primary was identical to this)

And so your problems began again once the secondary HDD was reconncted? I wonder do you have enough power supply wattage to run that lot?

I doubt it's the game - that's probably coincidence. Have you updated all drivers for motherboard chipset, graphics card, sound and ethernet/LAN?