I've having this exact same problem right now and have to change them manually in my autoexec.cfg file. Here's what I have right now to max out all effects:
- set cl_playintro 0
set ui_skip_eamovie 1
set ui_skip_titlescreen 1
set ui_skip_legalscreen 1
seta com_maxfps 999
seta r_swapinterval 1
seta r_mode 9
seta r_picmip 0
seta r_subdivisions 3
seta s_khz 44
seta cg_shadows 2
seta cg_effectdetail 1.0
seta r_lodviewmodelcap 1.0
seta r_lodcap 1.0
seta r_lodscale 1.1
set r_texturemode gl_linear_mipmap_linear
I still haven't figured out how to change the volumetric smoke to on, though. Its kind of pissing me off.
Here are my specs:
FX 5900 Ultra (using 44.03's)
SBLive!
P4 2ghz
Intel D850MVL mobo
PC800 ECC 512mb ram
XP Professional