Is it like a musty smell or proper rotting flesh? If the latter I'd check your engine bay and underside for road kill. There have been instances were cats have clambered up inside the engine bay sometimes... I'll leave you to fill in the blank!
Does it happen when you turn the aircon off then back on again? It could be the dreaded mold in the pipes, which can be cleaned out with an aerosol type system available from Halfords/Ebay/Web. Used it on mine a few times, works well.
It's fairly easy to do. Just get in the passenger footwell. Reach up behind the glove box and you will feel a foam covering. This is held on by two thumb screws. Remove the screws and the foam and you will see a plastic cover. Slide this to the left and remove it.
Then carefully remove the pollen filter. If it's anything like mine there was a fair bit of rubbish, dust and corn and other seeds which will empty all over the carpet.(I had just spent hours vacuuming too).
The filter is about £11 inc Vat so it worth doing this anyway if it hasn't been done on a 55 plate car.