There would be no difference in how you start duplicacy, except, perhaps, permissions.
How are you starting the bat file? Are you using windows “Task Scheduler”? What user is scheduler running your bay file as? Local user? Admin? System user?
I’m also suspecting you might not be changing directory properly (haven’t used windows in a while but just stating disk name in the file might not be enough? I’m probably wrong, but just in case). I would add /d to your cd command to actually cd to the path:
cd /D d:/data
duplicacy backup -stats
Or you can directly schedule duplicacy in the task scheduler — you don’t need intermediate files, even though either approach is equivalent.
How much ram is duplicacy using when it is appears to be stalled, and is there disk activity?
And lastly, what filesystem is on the disk D:, and any reason why are you not using VSS?