I promised that I would post the outcome of my research here.
Although the outcome is still on-going I found a work-around, not a solution, for the problem.
After much tinkering I did manage to recompile PHP with native gd.
I moved php source to /usr/src/php-5.2.10 and typed
./configure --with-gd=shared --enable-gd-native-ttf \
had to get rid of some errors related to missing libraries, which I installed.
Finally it configured.
Then make, make test, make install, make clean.
BUT...Drupal still complains about wrong version installed.
I am not the only user with this problem, I have read in the forums that others tried and failed the same way.
I have come to the conclusion that this is a bug.
As such I will file it with Ubuntu.
The work-around is simply to disable GD and work with ImageMagick.
No more warnings.
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