Same here (Gnome3, Unity). It works fine only when I click on "Friends" from "View" menu.

Interesting fact is that on KDE4 friendlist window is not even shown in foreground.

It was already reported on valve forums:

http://steamcommunity.com/app/221410/discussions/1/846939071417218739/
http://steamcommunity.com/app/221410/discussions/1/846939071113827967/
http://steamcommunity.com/app/221410/discussions/1/846939071304568236/

Gnome Shell version: gnome-shell 3.4.1-0ubuntu2
Unity version: unity 5.18.0-0ubuntu1
KWin version: kde-window-manager 4:4.8.5-0ubuntu0.2
Compiz: compiz-core 1:0.9.7.12-0ubuntu1

Terminal output:

ExecSteamURL: "steam://open/friends"

Entering steam steam://open/friends in terminal gives same result as clicking on "Friends" button. Window shows up but doesn't have focus and it behaves like it was transparent. All events are consumed by main window instead of friend list.

System Info output:

Processor Information:
    Vendor:  GenuineIntel
    Speed: 2400 Mhz
    2 logical processors
    2 physical processors
    HyperThreading:  Unsupported
    FCMOV:  Supported
    SSE2:  Supported
    SSE3:  Supported
    SSSE3:  Supported
    SSE4a:  Unsupported
    SSE41:  Unsupported
    SSE42:  Unsupported

Network Information:
    Network Speed:  

Operating System Version:
    Ubuntu 12.04.1 LTS (64 bit)
    Kernel Name:  Linux
    Kernel Version:  3.2.0-35-generic
    X Server vendor:  The X.Org Foundation
    X Server release:  11103000

Video Card:
    Driver:  NVIDIA Corporation GeForce GTX 260/PCIe/SSE2

    Driver Version:  3.3.0 NVIDIA 310.14
    Desktop Color Depth: 24 bits per pixel
    Monitor Refresh Rate: 60 Hz
    VendorID:  0x10de
    DeviceID:  0x5e2
    Number of Monitors:  1
    Number of Logical Video Cards:  1
    Primary Display Resolution:  1280 x 1024
    Desktop Resolution: 1280 x 1024
    Primary Display Size: 13,31" x 10,63"  (17,01" diag)
                                            33,8cm x 27,0cm  (43,2cm diag)
    Primary Bus: PCI Express 16x
    Primary VRAM: 896 MB
    Supported MSAA Modes:  2x 4x 8x 16x 

Sound card:
    Audio device: Realtek ALC883

Memory:
    RAM:  3954 Mb

Miscellaneous:
    UI Language:  English
    LANG:  pl_PL.UTF-8
    Microphone:  Not set
    Total Hard Disk Space Available:  290058 Mb
    Largest Free Hard Disk Block:  28753 Mb

Installed software:

Recent Failure Reports:
    Thu Jan  3 13:04:55 2013 GMT: file ''/tmp/dumps/assert_20130103140446_2.dmp'', upload yes: ''CrashID=bp-ca9b0698-6e9d-421d-aa3f-b195c2130103''
    Thu Jan  3 13:14:45 2013 GMT: file ''/tmp/dumps/assert_20130103141439_1.dmp'', upload yes: ''CrashID=bp-fb781ed2-75ac-436a-9cdf-2e34f2130103''

Please see my steps recorded on screenshots. In my case this "Friends" window behaves like it wouldn't be top window.

When you say "not in focus" what do you mean? Is it visually different? Are you talking about keyboard input? Are you saying things don't highlight or work when using the mouse on items in the window?

In my case UI elements are not highlighted when mouse is over them. There is no keyboard focus as well. And nothing really works on this window since it hides wherever I click on it.

Friends windows works fine only when it's accessed from "View" submenu or I when main window doesn't cover friends window.

Additional Screenshot:

I've updated client. And I confirm that the issue is fixed in Unity, Gnome3.

But there is still another issue on KDE4 I mentioned before:

Interesting fact is that on KDE4 friendlist window is not even shown in foreground.

Steps:

1. Open Steam
2. Open Friend list
3. Move friend list behind main window.
4. Activate main window
5. Click on "View friends" or "Friends" from "View" menu
6. You should notice that nothing happens (Window is not shown in foreground or active)

It works fine when friend list is initialy closed, then it pops out and works correctly.

The last update seems to have fixed it for me too on Mint 13 Cinnamon and Ubuntu 12.04 Unity.

@gdrewb-valve
It's KDE-specific issue. It works great on Unity and Gnome3 after last update.