For clarification, the second image has "show bones" ticked. There should be more bones than just the one.

Moreover, when I tried to compile the model, no bones besides that one would be recognized.

Does your QC have a $staticProp command? if yes, that command strips the bones from a model and makes it a static prop.

There is no static prop line in the .qc

Here I'm pasting a .qc from a different model, but it is having the same problem. If you can spot something let me know.

// Created by Crowbar 0.64

// Stored modelname (without quotes): "v_9mmhandgun.mdl"
$modelname "v_9mmhandgunn.mdl"
$cd "."
$cdtexture "."
$cliptotextures
$scale 1.0

$bodygroup "studio"
{
studio "glock_reference"
}

$flags 0


$attachment 0 "ber_body" -9 2.8 0
$attachment 1 "ber_body" -3 3.5 0

$cbox 0 0 0 0 0 0

$bbox 0 0 0 0 0 0

$hbox 0 "base" -37.029636 -34.843513 -12.4068 0 0 12.4068
$hbox 0 "ber_body" -8.86 -3.5 -0.74 2.04 3.16 0.76
$hbox 0 "ber_mag" -1.24 -3.87 -0.59 1.4 1.98 0.61
$hbox 0 "ber_slide" -7.03 -0.59 -0.71 2.85 0.97 0.73

$sequence "longidle" {
"v_9mmhandgunn_anims\longidle"
fps 30
}
$sequence "idle_1" {
"v_9mmhandgunn_anims\idle_1"
fps 30
}
$sequence "idle_2" {
"v_9mmhandgunn_anims\idle_2"
fps 30
}
$sequence "fire1" {
"v_9mmhandgunn_anims\fire1"
{ event 5001 0 "11" }
fps 30
}
$sequence "fire_last" {
"v_9mmhandgunn_anims\fire_last"
{ event 5001 0 "11" }
fps 30
}
$sequence "reload_empty" {
"v_9mmhandgunn_anims\reload_empty"
{ event 5004 8 "weapons/glock_magout.wav" }
{ event 5004 30 "weapons/glock_magin.wav" }
{ event 5004 47 "weapons/glock_slideforward.wav" }
fps 32
}
$sequence "reload" {
"v_9mmhandgunn_anims\reload"
{ event 5004 8 "weapons/glock_magout.wav" }
{ event 5004 30 "weapons/glock_magin.wav" }
fps 31
}
$sequence "deploy" {
"v_9mmhandgunn_anims\deploy"
fps 30
}
$sequence "idle_3" {
"v_9mmhandgunn_anims\idle_3"
fps 30
}



Thanks.

Are the bones weight painted to the mesh and an armature modifier added in Blender so the bone work in Pose mode?

Yes. When I import the animations to blender they play out fine, however it seems the bones are missing in compilation.

You're using a $scale command with a factor of 1, Why? You're not increasing or decreasing the scale. That said, are the transforms between armature and the mesh objects the same in Blender (or your 3D editor), Location 0, 0, 0 Rotation 0,0,0 and Scale 1,1,1? What game are you exporting for and compiling to?

This is for Half-Life 1.
I removed the redundant $scale command and this problem is still present.