The same behaviour will occur when using steam in the background and a notification pops up. Focus will be stolen from your current application for the duration of the notification and returned once the notification disappears.
It's not only the notifications that steal focus. The main Steam window also does this. For example, if you switch to another application while Steam is logging you in, the main Steam window will steal focus from whatever you're doing as soon as you have been logged in.
Maybe a related issue: login and exit dialogs are on top of every other window (using KDE). This is annoying when Steam takes a long time syncing data, as these dialogs stay in the middle of the screen and cannot be moved or hidden.
On Ubuntu 12.04, 32bit, with Nvidia & ATI cards:
I sometimes play FTL (as a standalone download from developer's website, not from Steam) in a window with Steam also running in another window in the background. Every time a Steam notification pops up, I suddenly can't control anything in FTL, nothing responds, and only after a bit of struggling do I get control back (I think as mewt666 said, you regain control whent he notification disappears). I lost at least one spaceship this way, so I just quit Steam and never have it running while I'm playing FTL.
Also, I sometimes have multiple chat programs open. One time I was holding a Skype and Steam chat simultaneously and while I was typing into the Skype window, my Steam conversation partner posted something and suddenly everything I was typing into the keyboard went into the Steam conversation window instead of the Skype conversation window.
let's just say steam handels windows very poorly. tooltips, notifications, menus and real windows all steal the focus, resize and repaint them self and all that stuff window managers were invented for. somebody didn't read freedesktop.org...
We're aware of the focus stealing problem and are working on it.
Focus stealing by notification popups is fixed and this fix will be in the next update (after New Years).
Focus stealing on startup is not yet fixed. This is still on our list.
Just to add this in while it's running in KDE (Kubuntu 12.10) lets say i close Steam but it's really minimized since minimize and close on Steam do exactly the same?! I then browse firefox and open a menu, bam my cursor changes to the same weird backwards pointer I get over the Steam window.
I still have this glitch... Annoying when ingame in a non-steam game
Nothing extracted yet.
I can't figure out a way to reproduce this, but it seems sometimes Steam notifications steal the focus form the active window and instead send it to an open Steam window, usually a chat window or something. I noticed it last night when I started TF2 and for some reason the in game overlay did not start (minor issue, it worked after starting TF2 again) but every time someone on my friends list came online or started playing a game, or even if a group made an announcement TF2 would minimize and I would be typing into a chat window.