I'm a little surprised at this. Apart from the initial corny taste, which usually dissipates after just a couple of smokes, my cobs all taste pretty neutral. Nonetheless, I have a few ideas:
First, what kinds of tobaccos are you smoking in them? I find cobs work best for Virginias and Burleys, not quite as well with Perique, and they just don't work for me at all with Latakia or Orientals. I much prefer the flavor of them in a briar, and they taste a litle off-putting to me in a cob.
Second, would you say the cobs had a stale or sour taste? When I get a new cob, one of the first things I do is roll up a scrap of sandpaper and sand the inside of the shank. They are pretty sloppy with the drilling, and leave a lot of fuzz behind, which I find can precipitate a little moisture in the stem and also act as a tar trap. I noticed this after smoking one of my first cobs several times. It developed a sour taste I couldn't shake with normal cleaning methods. Once I sanded off the fuzz, the nasty taste was gone.
Finally, if the flavor is bad toward the end of the bowl, you might be tasting the burning shank piece that extends into the bowl. It will char or burn off entirely after a while, but if you're smoking a little hot toward the bottom, it can be pretty unpleasant.
I hope this helps, and I hope you get to enjoy your cobs. They're the best smoking pipes for the bargain shopper, and a must in everyone's rotation, IMO.