This problem is fixed in CVS.
In the previous version (your version), the intermediate histogram used to draw the graph was systematically deleted when one point was added or modified.
TGraph::SetPoint method can be used to add a new point
to the graph. Removing of the histogram had a side effect
that following call of TGraph::Paint computed new ranges
for the histogram axes and new points became visible
even if they were outside of old axis limits. It seems
that now it’s user’s responsibility to update the axis ranges.