It's just like me to solve the problem as soon as I ask for help... It turns out that swapping the axes for the local coordiantes was the problem. What I did was work on the skeleton with the incorrect axes and then swapped them only after the world coordinates were calculated. Now the vertices attach and display correctly and no rotations are necessary for displaying the model.

Before, the bones were rotated very oddly, causing the mesh to look pretty funny and sometimes scary looking. I'm still curious why swapping the axes at the local level causes so much weirdness, but I don't mind being dumb and happy for now.

It's just like me to solve the problem as soon as I ask for help... It turns out that swapping the axes for the local coordiantes was the problem. What I did was work on the skeleton with the incorrect axes and then swapped them when only after the world coordinates were calculated. Now the vertices attach and display correctly and no rotations are necessary for displaying the model.

Before, the bones were rotated very oddly, causing the mesh to look pretty funny and sometimes scary looking. I'm still curious why swapping the axes at the local level causes so much weirdness, but I don't mind being dumb and happy for now.