Have baked all the weights in the Skin mod? If your morpher changed the shape of the base mesh enough then the mesh may have passed outside one of the envelopes. You can find the 'Bake selected verts' button(looks like an oven) under Weight Properties.
Thanks for looking into that further Mark. I've been looking into MaxScript to force correct evaluation and this seems to work. I can set everything up using the normal render settings dialogue and instead of pressing render there, I run this script. It'll run the range specified in render settings. There's no nice time…