I assume you've automated the naming format?
So the two first lines are something like this
gam user test.user1 show signature > Desktop/B-300/Signature_test_user1.html
gam user test.user2 show signature > Desktop/B-300/Signature_test_user2.html
So the target files are unique. If not, you will only ever get one signature into that file; the last one, since > overwrites previous content.
Have you tried using a CSV instead of a batch file?
Also, tried exporting all users to a single file and then splitting the content of that file instead?
gam all users show signature > Path/to/your/file.html