Usually when black mold begins to appear on these rubber door bellows, and cleaning does not remove it, you need to replace the bellow. Once the mold becomes imbedded in the rubber, it generally will not come off.
The following link explains step-by-step how to change the door bellow on a Whirlpool Duet series front loader:http://www.fixya.com/support/r3574186-installing_a_door_bellow_on_a_front_load
Replacement parts can be purchased at any of the following web sites:
I have found these sites to be reputable and provide great service. Prices differ between them, so shop and compare. The first three sites I've listed have helpful exploded view parts illustrations to assist you with locating and properly identifying the parts you may need.
This problem IS common, and has been duly noted by the manufacturers. That's why they have have recommended that you leave the washer door OPEN between washes to allow the drum to air out. The following link explains some of the common causes of front loader washer odors, mildew problems, mold problems and how to minimize or prevent them from coming back:http://www.fixya.com/support/r3608512-getting_rid_front_loader_mildew_odor
The number one cause, is associated with leaving the washer door shut all the time. The manufacturer recommends that you leave the door OPEN between washes to allow the wash tub to air out. This can prevent the build up of mold and mildew and will also minimize any odors that may develop. In addition, the constant applied pressure from the glass door being closed can cause the bellow to become stretched and mishapened. Over time, it will fail to properly seal and begin to leak
Also, there is ALWAYS residual water remaining in the drain pump and drain lines. This is NORMAL. Since this is the low point of the drainage system, water will always stay in this area. Leaving the door open will allow the washer to air out and prevent this water from becoming stagnant. In addition, the drain pump reservoir can collect dirt and debris over time. Periodically checking the reservoir will minimize odors. There is a follow on link provided that explains how to access and clean the drain pump.
Only use HE detergent. Using the wrong type of deteregent, or too much detergent can cause the build up of soap scum. Soap scum can also contribute to odor problems. Using regular detergent in these High Efficiency washers will also void any existing warranty you may have.
Read through the links provided and let me know if you have any questions. If the link does not take you directly to the instructions I provided, copy and paste the link to your web browser. I hope you find this information helpful.