"Before the upgrade, I had once pop-up asking for my key passphrase, then let me use this private key during my (home) session without further asking.. Now, when I try to connect to the host which even possibly want to check whether I want to present some key there, I got the pop-up. I even checked that I can connect to the host in question using plain xterm, and have usual password qiery."

I've been in similiar situation some time ago, when new gnome-keyring/seahorse (it started with one of the recent versions, don't remember exactly when, but definitely before 2.26 was introduced)

for some surely interesting reason insisted on creating a very own keyring every other reboot - while originally you were using one default keyring (let's call it "default") for storing your passwords, now gnome-keyring kept creating a new one named "login" and always set it as the default one.

That "login" keyring was even more special in that that nothing stored in it ever worked, it still kept asking for passwords and even then was not able to use them (and lost them on the next reboot anyway.. Maybe that's a feature, don't know, don't care). I've run into this on a few

different machines, every time I needed to open 'seahorse', get to Passwords tab, delete the "login" keyring, set the original "default" as the default keyring (first time I wiped them all and created a clean one to be sure, but as it turned out later, this wasn't needed), after that, passwords worked fine again. This procedure again and again for a few days/reboots, until seahorse miraculously stopped this madness and let my default keyring be, well, default (yes, just like that).

Anyway, if you weren't there yet, check seahorse gui for what keyring are you really using, maybe you've hit the same issue with the "login" stupidity..