It's more than likely some mysterious process taking over. It happens with some distros, on some hardware, sometimes. It's a rarity, but it does happens. Also, if you're at all skeptical of Linux, this problem transcends all Operating systems for all PCs.
To really know what's going on, open up a terminal (Kterm, xterm, gnome-terminal, etc.) and as root, enter ps -aux. Copy/Paste the output here please.