In earlier versions (2.x), the PIN entry window was in focus: just enter the PIN and go. In the 3.x version it is not, requiring manual selection of the PIN entry dialog.
- GPG4WIN 3
Is it possible that you have used a different pinentry in the past? Like the GTK one?
I've closed this as a dup because the pinentry-qt is the default one on Windows and T4123 describes your problem.