Is the actual view that you are publishing as PDF and DWG set to use grey scale pens?
So when you right click on the PDF and DWG in the Publisher list and then choose OPEN, they open with the grey scale pen set?
If not then you need to set the view to use the correct pen set.
It is possible to have a coloured view and then tell the PDF document options to save in greyscale.
This will produce a greyscale drawing but is not using the greyscale pen set.
If when you open the DWG in the publisher list it is using the correct greyscale pen set, then it is probably a setting in the DWG translator that is being used.
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