I have no idea how SD works, but in BFD2, there is a setting which you must switch in prior to exporting/bouncing - it's referred to as the 'offline' button.
Could SD have something similar to this?
I know if I forget to engage this, BFD2 will definitely drop out.
Also check your Midi prepare buffers - you might be getting Midi bottlenecks - whatever they are currently set to, double it and try again