I'm going to have to watch the movie again apparently. I did think you might be referring to that 4-note motif for Sirius/the Grim. I didn't count it because I don't feel it's developed enough to really be considered a theme.

> Pettigrew's Theme is played on the harpsichord. It contains nine notes,
> but the first six are the same. Unfortunately it never appears on album at
> all, but it's played many times in the film with reference to Pettigrew.

> The Sirius/Grim theme contains four notes. It doesn't appear on album much
> either, but you can hear it at 1:35 in "Quidditch, Third Year".
> The immediate start to that same track hints at the theme, as well. It is
> heard in the film as Harry and Mr. Weasley discuss Sirius Black and when
> Sirius steps out from behind the door in the Shrieking Shack.

> That's not true. It appears again when Harry and Hermione fly on Buckbeak
> to save Sirius from the tower at the end of the film. There is also a very
> brief hint to it in the film after Harry and Hermione go back in time.
> Hermione realizes that Dumbledore wants them to save Buckbeak too, and
> Buckbeak's Theme is reprised very lightly and briefly.

> It's just the main theme of the score, probably intented to represent the
> somewhat playful darkness of the film.

> Hedwig's Theme appears in "Lumos", "Secrets of the
> Castle", "Mischief Managed", and "A Window to the
> Past". There's the scene in which the season changes to winter, which
> is not on album. The theme is also played seconds before Lupin changes
> into a werewolf. "The Whomping Willow and the Snowball Fight" is
> based around a variation of Hedwig's Theme. But you're right about the
> Nimbus/Flying theme.

> It seems like these are non-thematic, but some of those are based around
> variations of the other themes. "Quidditch, Third Year" contains
> variations of the Double Trouble theme, while "The Whomping
> Willow" contains Hedwig's theme variations. But the others ones you
> mentioned, as far as I know, do not contain themes. I wouldn't be
> surprised if they are based around variations of themes, though.