try using the lm fonts instead of cm-super and you also get much more smaller files.
http://www.tex.ac.uk/cgi-bin/texfaq2html?label=uselmfonts
With the lm fonts you'll have the same problem: the 'A' and the 'i' are shown under the baseline until you set the magnification up to 150%. There is a bug entry for this on the following page:
http://pc52.ifw.ing.tu-bs.de/~harders/latex/lmodern.html
