When you restore down the Toad window, the Script Editor's vertical scroll-bar slider is not in view. This is mainly due to the scroll bar's top arrow being out of view.
See attachment: 679174_ScrollBarSlider.JPG
Waiting for fix in a future release of Toad for Oracle.
To see this issue clearly you have to do the following.
1. Find a table that has many columns and rows
2. Set the following
set pagesize 50000;
set linesize 500;
3. Run a "SELECT" statement using F5
4. Click on the "Restore down" button for Toad
Note: Step 2 is not necessary. It is only there to force vertical scroll bar to show up.