Is it an older one? Do you remove the filter media and take apart the filters removable parts ( intake tube, impeller, etc.)and brush them clean. Sounds like either gunk or something is stopping the impeller from rotating or for some reason the intake tube is not seating properly to the intake. If you haven't cleaned your filters moving parts in a while or ever, remove the cartridges and place them in a ziplock baggy with somew aquarium water. Use a clean bottle brush that is small enough or aquarium brushes or a new toothbrush works fine for this purpose. Make sure to remove all gunk from the impeller. Also scrub the inside of the impellers housing in the filters body. Is it possible something is causing the intake tube to vibrate away from the "seat"? Is the intake tube cracked?

First not sure which whisper filter you have?

(here is a link to a guy who works in business who has comments on various filtration systems)

http://www.americanaquariumproducts.com/Aquarium_Filtration.html

I will assume basic with propeller, if not following is mute point, lol. I have learned to follow the filter maintenance instructions religiously, lol. That said, I don't use the filter cartrages but make my own system ie bags filled with charcoal, other media with sponge to make sure no water leakage.

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Do you clean all the parts with each cleaning. You have to get one of those scrub brushes, and scrub down into the propeller area. Take out the propeller and (I find tweezers will do the trick)... take the tweezers and pluck strands of whatever have wrapped around the propeller - both ends. I have found when my filter stops running this is the main and usually only cause. Little hairs from wherever (cat, filter floss) get entangled around the propeller and eventually it just stops. You will be amazed at how much comes out when you start getting rid of it. Both ends.

Tap filter upside down to make sure no media or charcoal or bits of anything have not gotten stuck down in well of propeller area. Clean every nook and cranny you can think of. sometimes if you've had a while the rubber thing on end of propeller (if same as one I have) gets bent out of shape (esp if moving it up and down) so check this as well, and try to bend back to shape it's supposed to be in. (parts can be replaced)

I know what you mean by moving intake up and down, I often have to do this when I am sure all is cleaned, not sure why but suspect parts (propeller little rubber thing) is just run down. I often have to mack it down hard. (force it into proper area) I've had mine for several years now, probably longer then I think. As I have not replaced any, so more then five years?

So, take all apart in sink area, and clean all. I start it running in sink area to double check before adding filter media. (any tub or bowl that you can fill with water and hang on filter to edge will work).. Also, I often note I have to get it running in tank before adding media! They are often hard to get restarted, sometimes tilt away... but eventually they start. Too much time spent with these and I dread changing, but must be done, lol. Often it runs in sink area, so I move to tank, then it stalls. ARRGGHH! So I move parts up and down as you do, remove filter (I have in filter bag) et al, then tilt here there and eventually it starts up again. Just the design I guess. The link I enclosed has much information on different filters.

(the fluval canister is worse) Hope this helps some, Sherry

I pretty well concur with what both Woe and Sherry have suggested as being the reason for the problem, but suggest you go further.

Whisper's are really easy to clean, because you can pop the motor off the bottom and clean the case and tubes with total submersion in hot bleach water, which will sanitize the interior of the filter and melt off accumulated algae.

Also, don't be surprised if a hair you find wrapped around the impeller shaft is one of your own. It's amazing what can fall into an aquarium and eventually be drawn into the intake tube of a power filter.

The best time to give a power filter a through, back to new cleaning, is at a water change. With fresh water, the fish can go without the filter for the time it takes to clean it.

Bleach is perfectly safe if used properly, which simply means through rinsing. Once the filter pieces are rinsed throughly under running water then left to soak in water treated with a chlorine remover for a few minutes, they are safe to reassemble and put back to use on the tank.

If you are still concerned, use a hair dryer to get all of the parts dry, but it really isn't necessary, especially with fresh charcoal being run through it.

Once all of the parts are as clean as new and the filter reassembled, if the problem persists, then one of those parts is broken, because if all parts are intact and reassembled correctly, that type of power filter either works perfectly, or not at all.

I am a novice at this. I finally figured out that the plastic filter holder disconnects from the motor section.
The motor section then can be pulled apart into 2 pieces to expose the impeller, which was full of gunk (and hair!)