After the war, many German films were shown in the USSR, popularly known as "trophy films", this included the 1944 "The Woman of My Dreams" which was shown until mid-1950s.
At the same time the Soviets staunchly insisted on international ban on "Munchhausen".
The official pretext I believe was that it showed Munchhausen to have an adultery with Russian empress Catherine the Great which was perceived as anti-Russian. But this is quite surprising given that
The Soviets anyway had negative attitude towards Russian monarchy.
The empress anyway was known for adultery and having many lovers and favorites.
The story is told from the person of Munchhausen who is a known liar and exaggerator which hints the story may be an invention by Munchausen similarly to flying on a cannon ball and travel to the Moon.
The other version or real motives may be that of anti-Semitic overtone regarding Jewish-Italian count Cagliostro. Cagliostro is portrayed with a vampire-like face and the hint that he is Jewish is quite transparent, although never mentioned directly. In one scene he even says that Munchhausen's nose profile is better suitable for printing on coins.
But this scene could be easily cut off and in the second encounter with Munchhausen Cagliostro is portrayed differently: as a talented medic and scientist, expert in art and man of honour. The plot features a deep friendship between Munchhausen and Cagliostro so that Munchhausen even came to his friend to warn him about threat of arrest by the authorities. Cagliostro says "the Kanzler himself pursuits me". Although the Russian Empire had an office of State Kanzler at the time, this is a transparent hint at Hitler. Cagliostro thanks Munchhausen, gifts him an eternal youth and a ring of invisibility, becames invisible himself, pushes the Kanzler's soldiers who came to arrest him and disappears.
That said the film in general does not seem to contradict the Soviet ideology very much. Other scenes feature a corrupted Venetian doge which remarkably resembles Mussolini and uses inquisition secret police in an attempt to kill Munchhausen. In one scene he talks to a scientist who says that he serves only the science and not politics. The doge replies "keep this misconception, it will be our trump".
In one scene the Munchhausen's lover gets be imprisoned in a monastery by her brother, which is perceived as a tragedy. It adds some an anti-religious feeling to the film. In another scene the sultan secretely drinks alcohol and says to Munchhausen that he does so when nobody sees.
In yet another scene when the new wives to the sultan's harem are tested in military conscription like manner a black woman is shown to have better teeth than a white one, so that the white one is envy.
One more reason may be that Munchhausen explains his own theory of subhumans. According to him, anybody who does not know the principles of the universe, how the stars move and other scientific truths can be called a subhuman. This does not convey any racial meaning and shows a pro-scientific attitude which was very characteristic for the USSR propaganda as well. So I doubt this could be the reason.
So what was the actual reason and why?