Most likely the number of lines output to the Command Window exceeds the command window scroll buffer, which by default is 5000 lines.
You can increase the command window scroll buffer as follows: On the Home tab, in the Environment section, click Preferences. Select MATLAB > Command Window, and then increase the setting for Number of lines in the command window scroll buffer.
Increasing to 10000 lines will be sufficient to see all the output from this particular script. However, you may consider whether you really need to output entire arrays to the Command Window while the script is running. Maybe just seeing the first 10 rows and last 10 rows is enough, e.g.
pqrAndrSol([1:10 end-9:end],:)
or maybe just seeing the size is enough
size(pqrAndrSol)
or
whos pqrAndrSol
Of course, since it is a script, the variables exist in the workspace it's run in after the script is done running, so at that point you can inspect any variable however you like (outputting all or part of it to the Command Window, viewing it in the Workspace Browser / Variable Viewer, etc.).
