When you join two objects, the first selected inherits from the last selected (aka "Active object") a lot of properties, like modifiers, transform parameters, shading, and so on ....
Modifiers in particular are often acting in obj mode and disabled in edit mode (you can change this behaviour with modifier's little buttons near their names).
When rigging it's better to have some standard parameters, so, to start fresh and clean, delete all armature and subsurf modifiers, apply mirror, bevel and solidify modifiers if present, then join the two mesh, move it to the exact center of the scene, make all edit adjustments you need and apply All Transform in obj mode (Ctrl A).
Move the rig so that every bone is in the right spot and Apply all transform in obj mode (Ctrl A again).
Now you can bind the mesh to the armature (Ctrl P > with automatic weights) and add a Subsurf modifier if needed.