Using the latest installer I did a fresh install of Gpg4win on a Windows server, installed a secret key and then attempted to select multiple files in Windows Explorer and use Decrypt & Verify.
The UI showing decryption progress was shown, and all the files were successfully decrypted. When decryption had completed, I clicked Save All. At this point, only one of the decrypted files was actually saved.
I retried, and also tried using the Kleopatra UI to start the decryption process, with the same results. Decrypting a single file works fine. Afterwards I uninstalled 3.0.3 and re-installed 2.3.4 and the multiple file decrypt worked fine.
OS: Windows Server 2012 R2 Standard