Presumably the underlying script hasn't been properly updated or there is a bug. In the first case updating the script to include the dialog options would solve the issue.
Hello, what is the version of Photoshop that you are using? (to pinpoint which version might have a bug, if there is one)
Hello, I wold first try and install PsCC 2017, to see if the bug has been squashed. You can select to keep the previous version installed.
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Actually here is what I figured out.
I have updated to CC17 but the reason it wasn't working was because you need to go into save for web, and change the setting for PNGs in there. Once that is set, then you can use the batch or, layer comp to pngs...and they will adhere to the correct settings. If you set the settings in only the command prompts they will be over written by the save for web settings...
seems silly but thats the fix