TL;DR Embarrassment and fear that has become worse as time goes on.

It was originally covered up due to wartime censorship laws in order to reduce enemy intelligence, as well as to keep public morale at home high. But mostly, it was due to the fact that was a huge embarrassment, scandalous, and reflected terribly on the British and Belgians involved, and it was deemed bad for relationships and cooperation between American soldiers and their allies.

After the war, the records were kept sealed by the British who'd said "The story of the Leopoldville does not reflect any great credit upon us, and I should be averse to disclosing it unless the need is very strong. To issue anything publicly in America might only serve to revive a controversy that would be better allowed to die."

In the late 50's, some US documents regarding the incident were declassified, but it was done quietly and wasn't really publicized or made known to the families. Likely to protect public opinion towards our staunchest allies in a rapidly deteriorating cold war situation.

It wasn't until the 1984 discovery of the wreck and the efforts beginning in 1993 by Allan Andrade to publish a book regarding the incident and spread public knowledge that it became an issue. Due to mounting pressure, the British released some of their documents (but not all) about the incident, shortly before the book was published and no doubt to get ahead of the scandal. As far as I know, they still haven't fully declassified it.

If you want, I can provide some sources when I get home.