ATRflyer: The NG FMS will use the entered route winds on the RTE DATA page, or it will default to the cruise wind entry on the PERF INIT page. With neither of those supplied it will use zero winds for the predictions.
Once in flight, the the FMS will periodically update ETA's using the current groundspeed data. I'm not sure what the tolerance is, but it will update the ETA on its own, or whenever a selection is made that requires an EXECUTE, such as a "direct to". It will also update the predictions as it passes a waypoint.
If you play around with the RTA (Req'd Time of Arrival) page, without executing, you'll be able to see the ETA evolve with the winds (3rd or 4th line on the right side). To do this, enter the active waypoint in the RTA field, and it will bring up the current ETAs. With winds that are changing rapidly, and/or varying from the predicted winds, you can watch the ETA in line 3 or 4 change fairly quickly. If you're bored...
Hope that helps. But it sounds like you've got a pretty good handle on it.
Jonny