Apologies, I didn't notice the screenshots.
Yes, I see on your screenshots that the hatches appear to be different. When I do the same and look at the hatch pattern as selected in the ribbon, they are both the same hatch pattern, 'AR-SAND'.
It's interesting that they show up as different hatch patterns for you even though I did a matchprop. If you matchprop one to the other do they still appear as different patterns?
Note I am in ACAD 2014.
Both at the office on Friday and at home today, when I opened your attached file, both hatches showed as AR-SAND. I did not have a problem at the office on Friday, but I believe I was plotting to PDF, not PUBLISHing. I ran into the same inconsistent plotting of those hatches myself today using AutoCAD 2016 (oldest I have installed).
I played around a bit, and even tried it on a file I created. I do not have your CF_096.ctb file, so that may have some impact. I was finally able to get consistent treatment by specifying a named Page Setup in the Publish dialog (using monochrome.ctb), rather than using Default: None AND changing the lineweight on the layer from 0.00 mm to 0.05 mm. Your mileage may vary, particularly when using your own CTB file. The image shows the settings I used for the named Page Setup in AutoCAD 2016.
Yes, I am able to work around this by publishing to a page setup with a PDF plotter specified.
The problem does not seem to be specific to the ctb file; I have the same graphic issues when specifying a ctb of 'None'.
What I am really wondering is if this is just an AutoCAD bug, or if there is some setting that I am missing in the AutoCAD publish dialog or somewhere in the AutoCAD PDF driver properties.