Meredith, what kind of filter do you have?
I have Penguin Minis and I just rinse the crud off the cartridge in some tank water. Only when the fibrous pad starts wearing thin, do I splurge for a new filter. I have light bioloads and change 40 - 50% of the water weekly, so I don't concern myself about the carbon in the cartridge.
As far as the smell, most tanks have a rich earthy odor - it really should not be unpleasant. Musty, strong, and mildewy doesn't sound good. Perhaps you're overfeeding or need more filtration, or more frequent gravel vacs? How often do you change the cartridge? Maybe you could try rinsing off the decaying crud between changes like I do.