Many, many programs can do this, especially in windows 7 which unlike XP does not have a setting to prevent windows from stealing focus. Antivirus(or viruses), java/google update, even parts of windows. Close all running programs and put your AV on game mode before playing fullscreen. The taskbar bug mentioned is most likely Aero related. And if you're playing games with Aero enabled you're DOIN IT RONG.
Disable aero, set Windows Update to "Notify but don't download or install",
Do a virus scan and then get
wait for it to load, then make sure options>"hide windows and system entries" is enabled, disable anything sketchy after googling it. Play around with it and use "disable" instead of "delete" unless you know exactly what you're disabling. Then finally
ctrl+shift+escape and check running processes. There shouldn't be alot of processes under "administrator". On my system I've got two for Setpoint, one for ACE, one for CCC, three from firefox,explorer, dwm, taskmgr and cfp(my AV). There shouldn't be much else on there.