@rainforest1155
No, I couldn't reproduce it with Opera Stable version 21.0.1432.67.
Have you modified shortcuts in your Preferences file?
@tjamroszczak
Ah, I was still on 21.0.1432.57 and updating to 67 seems to have fixed the issue. Thanks for your quick assistance!

I also encountered some changes related to shortcuts and found a workaround that doesn't require to actually change the default Opera shortcut. In my case, manually setting up the shortcut in the preferences using the same shortcut actually fixed my issue.
So in your case, instead of setting up a different shortcut, try entering the default one in the preferences:
"Keybindings": { "Basic": { "ParentDirectory": [ "Ctrl+Backspace" ] } },

I haven't tested that, but maybe you're seeing the same root issue as I did and it works for you too. For reference, here's the thread I posted in:
https://forums.opera.com/topic/2723/opera-21-suddenly-overriding-web-site-keyboard-shortcuts/3

@tjamroszczak: You can test this here:
http://www.openjs.com/scripts/events/keyboard_shortcuts/
Scroll down to "live evaluation" and set up CTRL+U or CTRL+R in the code. You should see that the shortcut takes no effect and instead Opera's default action is executed.

Interestingly, if I change the default Opera shortcuts to Ctrl+Shift+U and Ctrl+Shift+R respectively and test it again using these shortcuts, the javascript alert box is executed fine. So it appears Opera only enforces its built-in shortcuts as long as they're not user defined in the preferences.

EDIT: In fact, this just gave me the idea for a perfect workaround - I've now manually added the default shortcuts to the preferences file:
"Reload": [ "Ctrl+R" ],
"ViewSource": [ "Ctrl+U" ]
and now Opera no longer seems to interfere with the above test page or the desk.com site.

Still, would be nice to get this resolved. Perhaps the folks in this thread:
https://forums.opera.com/topic/2564/opera-21-annoying-new-behavior-with-ctrl-backspace/12
are seeing the same issue just with a different shortcut?

With the update to version 21, shortcuts on web sites are no longer working if they coincide with Opera keyboard shortcuts.

For example, in the desk.com agent screen I use for work, there's a shortcut to update a case using CTRL+U and one to resolve a case with CTRL+R. Prior to the latest update, those worked fine, but now they open the page source / refresh the page respectively.

Is there any way this can be returned to the previous behavior on where web site shortcuts are the first priority and only if the site doesn't use the shortcut, would it be passed on to Opera.

Thanks,
Sebastian

PS: I'm aware of the option to manually edit the preference file to change the Opera shortcut, however I generally like having CTRL+R to refresh a page as that's the default shortcut for all browsers.