In 25.0.91 there is a change in behaviour when opening gpg encrypted
files.

Previously (Emacs 24, Emacs 25.0.90) when the command that caused an
encrypted file to be opened was issued from the minibuffer, e.g. `C-x
C-f myfile.gpg' or `M-x gnus' (which on my system opens
~/.authinfo.gpg), then the password prompt was displayed in the
minibuffer. (I don't know what the behaviour was when menus were
used; I don't use menus for opening files or starting Gnus.)

This was consistent the "normal" polite behaviour in Emacs: when the
user initiates an action from a command typed in the minibuffer, Emacs
interacts with them in the minibuffer; when they initiate an action
using graphical controls, Emacs interacts with them in graphical
dialogs.

Now the prompt for the gpg password seems to be always in a graphical
dialog box, even when the user was interacting with Emacs from a
keyboard in the minibuffer.

[Additionally, the offending dialog box doesn't make it clear who is
asking for the password nor for which file the password is being
requested(!), and furthermore, the dialog is almost system modal -- it
blocks the entire desktop environment (although virtual terminals can be
reached).]

A screen capture of the dialog box is attached. Note that it doesn't say
what file it is asking for the password for, and there's nothing to say
who is asking for the password.