If you are using PFPX or SimBrief you might need to apply a fuel correction bias. I found that on a typical 1:30h flight the captainsim uses about 1t more fuel than predicted by PFPX or SimBrief.
The longer the flight gets the closer the values will start to match the planned values.
In PFPX adding about 400kg for the climb and 500kg for the approach will give you about the correct fuel burn for the captainsim 757.

Agreed on the crossing restrictions, VNAV needs lots of improvements, especially on the speed management part!

I never had a violent breakout on approach as you said, despite over 100 flights with the 757 now.