He perceived the dangers from neighboring Zimbabwe, seeing dictatorial Robert Mugabe as living in a vanished age of imperialists and liberation movements.
But he was determined on "quiet diplomacy," avoiding a showdown that might precipitate civil war, forcing millions of refugees south.
There was one issue about which he appeared irrational -- AIDS. He belatedly abandoned his belief that it was not necessarily linked to HIV and has authorized massive anti-AIDS programs with international support.
But he still refuses to use his presidency to publicize and confront the problem, or to replace inadequate Health Minister Manto Tshabalala-Msimang.
His intransigence worried many old friends, including myself, who speculated about his motivation.
Was he exasperated by racist white critics who blamed blacks for vulnerability to AIDS? Or was he politically expedient, knowing many voters were also reluctant to confront the problem? Or was he too isolated to understand the reality?
As president he seemed insulated and defensive -- very different from the adventurous exile who enjoyed arguing with anyone. He appeared uneasy among crowds, reluctant to reach out.
Afrikaner satirist Pieter-Dirk Uys complained: "We've got a government of the people, for the people, by the people, led by a president who doesn't like people."
Mbeki's fiercest critics went much further: they thought that he was developing the paranoia that other African leaders had shown as they moved towards autocracy, and feared that, with his two-thirds majority, he would change the constitution to allow himself a third term in office in 2009.
Yet Mbeki has shown good judgment during most of his presidency, with the exception of his failure over AIDS.
He has retained his negotiating skills which held together his diverse, multiracial country and given it a stability few of his critics expected.
He remains essentially the same young exile I knew, an intellectual deeply influenced by liberal European culture and always aware of the limitations of power.
White South Africans will always expect him to show them special favors, but to preserve his leadership he must always show himself a true African. For without the support of the black majority he is lost.
After he has reconstructed his Cabinet, and delivered his inaugural speech next wee, we will see how successfully he can combine his English and African roots.
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