Character height change throws off alignment of bones to mesh.

[rbrandford]

I have a character (Darius8) where I am adjusting the height and if I import with the fix joint alignment option chosen, the height change is not reflected in the skeleton. It looks like a skeleton for someone 6' 4" overlapped with a character 5' 10". Is this a known issue, and if so, how can I get around this? Files can be supplied.