I wrote a how-to some time ago for installing the Orange Box. See section 8 which discusses setting Steam options: http://www.justlinux.com/forum/showthread.php?t=151354 I also found out later that installing DirectX 9.0c through wine pretty much killed my performance. I know the little hiccup you are referring to and I seem to remember that when I installed a fresh prefix of wine and this time DID NOT install DX9, things ran much better. Not sure if you have done that or not. I haven't played TF2 in some time so I'm not sure if that little pause still happens on my system or not. But it might be worth checking into the heapsize and dxlevel options.
