Be careful, the DXF format does not contain units, just values! A segment of length 2 can be interpreted as 2mm, 2m, 2 inches... It depends much more on the software that opens the DXF than on the one who created it!
If I were you, I'd look more for Draftsight than for BatchConverter. Default unit when opened... I don't know it, vaguely used several years ago...
On the other hand, I have used BatchConverter a lot and I have never had this problem.
It's the same menu but from BatchConverter. You then follow the framed windows in order (this may change something). What is the 1/1000 scale ratio? (m/mm conversion) or another scale?
For me Drafsight doesn't take into account the scale since you're always supposed to draw at a scale of 1:1 in the model. Edit: to see if it comes from document you can also export it in step, reimport it and then export it in dxf if the scale is good it probably comes from your model otherwise it comes from the conversion.