Collision Joints Improperly Working in Maps

I am currently working on a pack of props for a Binding of Isaac themed map. Some of the models I’ve made require $collisionjoints to work properly, however, every model with them appear to break when used in a map:

This is a screenshot from a testing map I’ve made, and as you can see, the collision mesh isn’t properly aligned with the door which has an animation to fall open. There are about 3 other models with collision meshes that are bugged, again, by the $collisionjoints perimeter. I can’t post them though because it would spoil some later parts of the map.

Does anybody know what’s causing this problem?

$cd "C:\Steam\steamapps\fissionmetroid101	eam fortress 2	f\models\props_isaac"
$modelname "props_isaac/Trap_door.mdl"
$model "body" "trap_door"
$cdmaterials ""
$cdmaterials "models\props_isaac"
$hboxset "default"
$sequence closed "td_closed" fps 30.00 loop
$sequence open "td_open" fps 37.50 
$sequence opened "td_opened" fps 30.00 loop
$collisionjoints "trap_door_phys.smd"

This is the .qc, if that’ll help at all.