If you're using the DDS Converter, the mip map option is under the options - on the right hand side, if I remember correctly. I typically mod the DDS files in PhotoShop C2 (saving as 32 bit), and generate any required mip maps that way. However, I have forgotten to generate them a few times, and was able to use the DDS converter to generate them.
Hope that helps!
(btw, what are you using to mod the graphics files, and what window are you trying to mod?)
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