Setting new keywords using PDFBox 2.0.16 inserts the data into the file (confirmed via the PDF Debugger and running a script in Acrobat), but the keywords are not displayed in the Acrobat GUI. This might be a bug of Acrobat itself, but it will be good to know why this is happening, and whether it can be solved.
Attached are a blank sample file created in Acrobat, with no metadata, a java file with the code I used, and the result of running it on that file. When I open the edited file in Acrobat (11.0.10) the Properties window is still empty. However, running the following code from the JS Console does print out the correct output:
I'm also attaching the same file after I've added keywords to in Acrobat, so the internal structure could be compared with what PDFBox does. I didn't see much of a difference, but maybe I missed something.