Sycraft . . . are you waiting for all the samples to load ?
My BFD3 takes a while to load all the samples, so I can't hit play right away, or there will be dropped notes.
I've done quite a bit of export / rendering with BFD3 in Sonar Platinum, and it works the same as X3e, so far.
Don't know what your system is like, but I try to keep all my sample drives defragmented for optimum performance as well.