I haven't verified the following fully, however I think it might be a problem that needs looking into. Perhaps someone else could try the same to confirm?
I designed a job to print with my left extruder. I then pre-heated te left side to 235 degrees, and executed print over USB.
As the left extruder was already sitting at the required temperature it was held there by S3D whilst the bed came up to 105 degrees. Once the bed reached temperature no further progress was made.
I think, but am not sure, that if the extruder temperature is already at the required value then S3D doesn't need to heat the extruder, and it goes into a loop which it never comes out of - because there is no event to suggest that the required temperature has been reached.
If I execute the same job without preheating then it works fine.