When I start tf2 in borderless windowed mode with the width and height set to the dimensions of the screen it starts one window border from the top of the screen. I can move it to the proper position and it is the correct size after that.

My launch options:

-novid -windowed -noborder -w 1280 -h 800

If it matters I am using a multi-monitor setup with no panel on the monitor in question (at first I thought it may be one panel width).

System Info:

Processor Information:
    Vendor:  GenuineIntel
    Speed: 2000 Mhz
    2 logical processors
    2 physical processors
    HyperThreading:  Unsupported
    FCMOV:  Supported
    SSE2:  Supported
    SSE3:  Supported
    SSSE3:  Supported
    SSE4a:  Unsupported
    SSE41:  Supported
    SSE42:  Unsupported

Network Information:
    Network Speed:  

Operating System Version:
    "Arch Linux" (64 bit)
    Kernel Name:  Linux
    Kernel Version:  3.7.4-1-ARCH
    X Server vendor:  The X.Org Foundation
    X Server release:  11301000

Video Card:
    Driver:  NVIDIA Corporation GeForce 9200M GS/PCIe/SSE2

    Driver Version:  3.3.0 NVIDIA 313.18
    Desktop Color Depth: 24 bits per pixel
    Monitor Refresh Rate: 59 Hz
    VendorID:  0x10de
    DeviceID:  0x6e8
    Number of Monitors:  2
    Number of Logical Video Cards:  1
    Primary Display Resolution:  1280 x 800
    Desktop Resolution: 2560 x 1024
    Primary Display Size: 13.03" x 8.15"  (15.35" diag)
                                            33.1cm x 20.7cm  (39.0cm diag)
    Primary Bus: PCI Express 16x
    Primary VRAM: 256 MB
    Supported MSAA Modes:  2x 4x 8x 16x 

Sound card:
    Audio device: Nvidia MCP77/78 HDMI

Memory:
    RAM:  3925 Mb

Miscellaneous:
    UI Language:  English
    LANG:  en_CA.UTF-8
    Microphone:  Not set
    Total Hard Disk Space Available:  227875 Mb
    Largest Free Hard Disk Block:  8211 Mb

Installed software:

Recent Failure Reports:
    Wed Jan 23 21:53:19 2013 GMT: file ''/tmp/dumps/assert_20130123165313_1.dmp'', upload yes: ''CrashID=bp-024062f6-a8a9-408b-9983-1e6d02130123''
    Thu Jan 24 18:08:28 2013 GMT: file ''/tmp/dumps/assert_20130124130820_1.dmp'', upload yes: ''CrashID=bp-9fbf9636-8cc9-4c33-b080-6c4e22130124''
    Thu Jan 24 18:08:36 2013 GMT: file ''/tmp/dumps/assert_20130124130833_2.dmp'', upload yes: ''CrashID=bp-58b53f04-a5c9-4272-b282-58fdb2130124''
    Thu Jan 24 18:21:50 2013 GMT: file ''/tmp/dumps/assert_20130124132145_1.dmp'', upload yes: ''CrashID=bp-bc9a6c9e-4b10-4905-8ce6-97fe02130124''
    Thu Jan 24 19:25:34 2013 GMT: file ''/tmp/dumps/assert_20130124142533_1.dmp'', upload no: ''Failed to open/read local data from file/application''
    Thu Jan 24 21:21:01 2013 GMT: file ''/tmp/dumps/crash_20130124162057_1.dmp'', upload yes: ''CrashID=bp-ffbf0f6c-b783-42ed-b278-9000f2130124''
    Fri Jan 25 03:02:15 2013 GMT: file ''/tmp/dumps/assert_20130124220206_1.dmp'', upload yes: ''CrashID=bp-42a89db2-ef2e-4926-8476-9f83c2130124''
    Fri Jan 25 03:02:23 2013 GMT: file ''/tmp/dumps/assert_20130124220219_2.dmp'', upload yes: ''CrashID=bp-b47c86b8-8c92-4eb1-ac5c-833d52130124''