GPA Error Unsupported Certificate

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The encryption key manager you can work in Ubuntu is seahorse. Is pre-installed in most Ubuntu versions (13.10 included).
Click on Dash and write: passwords , then open the passwords and keys program and you can manage all your keys from there.
Alternatively you can open a terminal (CTRL+ALT+T) and write:

    seahorse

above command will open the same window.

Read more about seahorse here:
https://projects.gnome.org/seahorse/

Read more about GnuPrivacyGuard(How to) here:
https://help.ubuntu.com/community/GnuPrivacyGuardHowto

If you want this specific program (GPA) then read also here:
http://ubuntuforums.org/showthread.php?t=1977872 (similar problems with yours, seem does not working well)

You can raise a bug report if you want about this specific program. How to report bugs, see here:
https://help.ubuntu.com/community/ReportingBugs

This guide about (seahorse and GPA) might helps you, also:
http://ubuntuforums.org/showthread.php?t=680292

Best Regards
   NikTh

Sadly this does not answer the above question about the error message in GPA .. Just because we can use another program does not mean the issue is fixed .. For instance due to some weird glitch I am unable to use seahorse since most of the options do not work ...

I have exactly the same problem.

I imported my keys using gpg in the terminal but even after you press Ok on the error message the keys won't show in GPA.

When I try to open preferences I get the same error as well.

When I close the application I get the following output in the terminal:
"""

(gpa:5436): GLib-GObject-WARNING **: invalid unclassed pointer in cast to 'GtkTreeView'

(gpa:5436): Gtk-CRITICAL **: IA__gtk_tree_view_get_model: assertion 'GTK_IS_TREE_VIEW (tree_view)' failed

(gpa:5436): Gtk-CRITICAL **: IA__gtk_list_store_append: assertion 'GTK_IS_LIST_STORE (list_store)' failed

(gpa:5436): Gtk-CRITICAL **: IA__gtk_list_store_set_valist: assertion 'GTK_IS_LIST_STORE (list_store)' failed

(gpa:5436): GLib-GObject-WARNING **: invalid unclassed pointer in cast to 'GtkTreeView'

(gpa:5436): Gtk-CRITICAL **: IA__gtk_tree_view_get_selection: assertion 'GTK_IS_TREE_VIEW (tree_view)' failed

(gpa:5436): Gtk-CRITICAL **: IA__gtk_tree_selection_select_iter: assertion 'GTK_IS_TREE_SELECTION (selection)' failed

"""

Unsupported Certificate error is connected with gnome-keyring. GPA needs to connect with gpa-agent. If you check yours exports in termnal GPG_AGENT_INFO - points to gnome-keyring. After this:

 $ unset GPG_AGENT_INFO
 $ eval `gpg-agent -v --daemon`

I was able to launch gpa without any problems. The GPG_AGENT_INFO - points to gpg-agent - that is what gpa expects.
I wrote simple bash script to launch gpa:

#!/bin/bash

eval `gpg-agent -v --daemon`

gpa

exit 0

I hope this will help you.

That did unfortunately not solve my problem.

I recently moved from Mint 16 to Ubuntu 14.04 and am I'm also having issues with GPA.

Although Daniel's solution works , I don't think it's particularly neat. I have tried to set up the same in my .profile script, but I can't seem to get it to work.

@zeromass
I also try to add some solution like this do .profile, bashrc, but nothing works.