Firstly you should be using ConvImX (on my beta page).
ConvIm is a general purpose "photo" image converter and doesn`t preserve alpha channels for extended bmp or DDS. ConvImX is an enhanced version aimed at formats that include alpha channels. Particularly game textures

DDS files are internally upside-down compared to bmp so will usually need flipping upside down when created directly from a bmp to keep the same mapping.
ConvImX has an option "Flip image data during conversion" which if selected will invert the image data during the conversion step.
However........
I can`t remember offhand if ConvImX automatically flips for DDS when coming from bmp so you should first try a small batch without selecting the option to see if it is auto-fixed. If the mapping is still wrong run again with the option turned on