I've tried it also with the vanilla server.cfg for cstrike. The same thing happens: the plugin doesn't pick up the value of the my_cvar in server.cfg when running with -console.
The command I used to start the HLDS instance doesn't do anything out of the ordinary: hlds.exe -console +log on -game cstrike -ip 127.0.0.1 +port 3000 +clientport 3000
server.cfg
// Use this file to configure your DEDICATED server.
// This config file is executed on server start.
// disable autoaim
sv_aim 0
// disable clients' ability to pause the server
pausable 0
// default server name. Change to "Bob's Server", etc.
hostname "Counter-Strike 1.6 Server"
// maximum client movement speed
sv_maxspeed 320
// 20 minute timelimit
mp_timelimit 20
sv_cheats 0
// load ban files
//exec listip.cfg
//exec banned.cfg
my_cvar 1
map de_dust
Changing the order of the my_cvar declaration in server.cfg doesn't help either, I've observed. Is it something else perhaps? It can't be just me experiencing this, now could it?