This issue may be related to #833.

Yikes, every numeric non-integer value has comma as a decimal separator.

VERSION 1,0

DESCRIPTION INFO_OPTIONS
{
"cl_corpsestay"
{
"#Cstrike_Corpse_Stay"
{ NUMBER 0,000000 600,000000 }
{ "600,000000" }
}

"mp_decals"
{
    "#Valve_Multiplayer_Decal_Limit"
    { NUMBER 0,000000 4096,000000 }
    { "300,000000" }
}

"max_shells"
{
    "#Cstrike_Max_Shells"
    { NUMBER 0,000000 -1,000000 }
    { "120,000000" }
}

"max_smokepuffs"
{
    "#Cstrike_Max_Smoke_Puffs"
    { NUMBER 0,000000 -1,000000 }
    { "120,000000" }
}

"fastsprites"
{
    "#Cstrike_Smoke_Quality"
    {
        LIST
        "#Cstrike_Smoke_Best" "0"
        "#Cstrike_Smoke_Medium" "1"
        "#Cstrike_Smoke_Worst" "2"
    }
    { "0,000000" }
}

"cl_righthand"
{
    "#Cstrike_Weapon_Alignment"
    {
        LIST
        "#Cstrike_Left_Handed" "0"
        "#Cstrike_Right_Handed" "1"
    }
    { "1,000000" }
}

"_vgui_menus"
{
    "#Cstrike_Buy_Menu_Type"
    {
        LIST
        "#Cstrike_Old_Style_Menus" "0"
        "#Cstrike_VGUI_Menus" "1"
    }
    { "1,000000" }
    SetInfo
}

"_cl_autowepswitch"
{
    "#Cstrike_Automatic_Weapon_Switch"
    { BOOL }
    { "0" }
    SetInfo
}

"hud_centerid"
{
    "#Valve_Center_Player_Names"
    { BOOL }
    { "0" }
}

"_ah"
{
    "#Cstrike_AutoHelp"
    { BOOL }
    { "0" }
    SetInfo
}

"hud_takesshots"
{
    "#Valve_Automatic_Screenshots"
    { BOOL }
    { "0" }
}

"cl_observercrosshair"
{
    "#Valve_Observer_Crosshair"
    { BOOL }
    { "1" }
}

"cl_radartype"
{
    "#Cstrike_RadarType"
    {
        LIST
        "#Cstrike_Transparent" "0"
        "#Cstrike_Solid" "1"
    }
    { "0,000000" }
}

}

I'm having the same issue, but not all the time.

BTW, a bit offtopic, but while we're talking of user.scr, if you could remove the "SetInfo" line from _cl_autowepswitch alfred, this would fix the cvar value change not being saved into config.cfg. It currently always stay at 1 in config.cfg, no matter if you tick or untick the box. After removing "SetInfo" it works fine.

Yes, renaming the old file worked but only after verifying the game's files it downloaded a new, properly formatted user.scr.