Cheese fondue usually goes clumpy if it is overcooked, or has had something acidic added to it (like lemon juice). If some of the cheese just has not melted properly, just put it through a blender and it will be fine. However if it's overcooked or separeted, it's better to throw it out and start again.
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If rice clumps after cooking it is generally because the rice is very starchy. To remedy this you can pour boiling water over the rice to rinse away some of the starch, then fork through it using a fork to fluff it up and remove any larger clumps.