hedwards: I assume the prohibition is the result of German bureaucracy not wanting to have to judge the difference between the uses of the symbol outside of limited educational use to see if it's adequately anti-Nazi.
More or less.
Basically, it all goes back to the infamous court case that resulted in Wolfenstein 3D's banning for its usage of "anticonstitutional symbols". It set the precedent all other video games had to follow afterwards, because no one in the industry really dared to challenge the court's decision.
Thanks to this, the USK outright refused to even rate games that featured swastikas until very recently.
Movies didn't have that problem (not to this extent, anyways). Indiana Jones and the Last Crusade was always rated "ages 12 and up" in its uncut form, while the point and click adventure based on the film had all the swastikas removed to get by. This is largely the result of a general moral panic regarding video games in Germany at the time (elements of which persist to this very day in politics and media). A truckload of fairly innocuous games were put on the index during the 80s, because they were "too violent" or they "glorified war". River Raid being one such game.