I haven't had time to dive in and figure out why this is happening, but the easiest fix is to do this:
1) Enable biped figure mode (t-pose)
2) Select your skinned mesh
3) Under "advanced" uncheck "always deform"
4) Align your skin mesh to the biped if it is not already aligned
5) Under "advanced" re-enabled "always deform"
6) Leave biped figure mode
This will fix the mesh scaling issue, but may not properly retain all mesh vertex skin weights...so some adjustment may be necessary. Hopefully I can just fix this in the future so the workaround is not necessary.
1) Enable biped figure mode (t-pose)
2) Select your skinned mesh
3) Under "advanced" uncheck "always deform"
4) Align your skin mesh to the biped if it is not already aligned
5) Under "advanced" re-enabled "always deform"
6) Leave biped figure mode
This will fix the mesh scaling issue, but may not properly retain all mesh vertex skin weights...so some adjustment may be necessary. Hopefully I can just fix this in the future so the workaround is not necessary.