That's odd - I haven't seen that problem before.
Are you rendering out an individual timeline or the Master Session?
The Master Session should have ALL of the media (including handles) - so you can easily watch through it to see if the handles are graded or not.
However, depending on how you brought in the media to the project, rendering out the master session may not be appropriate. Generally we always bring in the media via an EDL (with handles) using the "Add Media & Split", so that the Master Session only contains the footage we actually need.