can you monitor the temperature ?
Sounds like it might be getting up to temperature, and then not holding that temp.
You don't have a control panel on the front do you, can you print from s3d via usb ?
In which case that will show you the temps.
Could be as simple as a g-code command to keep the extruder hot going missing.
I know when the last time there was a s3d update it buggered up my profiles, so haven't updated to the latest version.

That's the only thing I can think of and I have had the same problem in the past.