I might try it, since the cleaner program didn't seem to solve the problem.
Could it be that my fan is not efficient enough?
If you have a relatively run of the mill PC, generally the fans in it are good, from my experience. Premade computers such as Dell or Gateway seldom have cooling issues. Dust, however, is not part of the PC system and will give you cooling issues, which is why Vekseid suggested the canned air. Dust, hair, and other debris get into vents and on fan blades, mucking up their efficiency.
However, if you're a chronic upgrader, you may have outgrown your cooling system. I'm told that your power supply will shut down if it's not up to the task of power demand, as well, but you might want to wait for someone else to check me on that, since I'm not a hardware junkie, just a tinkerer.
You can try going on newegg or tigerdirect and looking at additional fans and whatnot if you're worried about it. They have some nifty ones that I've been told work really well. Also, most cases are designed to vent best when they're properly closed and whatnot. For example, if you have a habit of leaving the side panel off of your PC, not only does it let in more dust and crap, but in theory it's less efficient with the fans and whatnot at cooling.
Basically I'm agreeing what Vekseid said, but trying to answer your question of 'why'.