I hope someone will be able to help me with this.

My Windows XP machine refused to boot. It goes until after finding the boot record on the disk, and then stops right there, leaving a blank screen. When trying safe mode, it stops while loading windows/system32/config/system.

After rebooting a few times (I tried all different methods - Ctrl-Alt-Del, reset button, turning off and then on, plugging out and in), it suddenly "agrees" to boot, and upon entering Windows it leaves a message "One of the files containing the system's Registry data had to be recovered by use of a log or alternate copy. The recovery was successful". Then Windows works normally until the next reboot - then the whole story repeats itself.

Initially I thought (as anyone would) that the problem was with the hard drive or Windows installation - but it keeps happening even after replacing the hard drive (with a brand new one) and clean installation of Windows.

Could it be a motherboard/CPU/RAM issue? But if one of those were faulty, wouldn't it stop the booting at a much earlier stage? How could that be explained?

...but it keeps happening even after replacing the hard drive (with a brand new one) and clean installation of Windows.

! Initially, I was going to say a drive controller issue, but if that was the case, I doubt a clean Windows install from scratch would be successful. So...

Hard Drive/Other Drives: Unhook all other drives, particularly any slave devices on the same channel as the hard drive. Also, check/swap cables. Running an exerciser like Hitachi Drive Fitness Test (http://www.hitachigst.com/hdd/support/download.htm#DFT) or long wipes with Darik's Boot And Nuke (http://www.dban.org/) can exacerbate intermittent errors.
RAM: Test ram for 24 hours with Memtest86.com (http://www.memtest86.com/).
CPU: They tend to work or not at all, hanging the computer.

Do you have another motherboard or power supply to try?