I'm bad at 'small' stories, too. (Which is why my comic is probably going to be nearing 100 pages before I get out of chapter 1... sob) But one thing that helps me is making sure each page I'm drawing is 'worth it' somehow. Each page should contribute something to the narrative-- either setting up a situation, furthering that situation, introducing new relevant information, or showing you an important aspect of a character. Don't try to cram too MANY 'worth it' things onto one page, though -- remember you usually only have 5-7 panels on an average comic/manga style page to get your story across.
Here's a small example of how I handled this in my prologue, which is the closest example I have to a 'short' story:
Page One: I introduced the reader to the main character, her culture, and the concept of the Song (which is an important part of the story).
Page Two: I explained a bit about what the Song IS, and how it fits into her culture.
Page Three: I show a fragment of a legend about someone who doesn't have the Song, and present it as a bad thing (which is also important).
Page Four: I set up the moment the character goes to learn the Song for herself.
Page Five: I show the moment the character is denied the Song.
Page Six: I show that the reasons why she was denied are unknown, and the repercussions this has on her.
Page Seven: I show the character moving on with her life, Song-less, and trying to fit into society, but always feeling a bit like an outsider -- which sets up the rest of the story, and eventually a life of adventure.
Seven pages. Each has a point. I give myself 5-7 panels on each page to build/make that point, but I make sure each page HAS at least one. So you could think of story-building as "What 'points' do I need to make? How many 'points' does that make? How do I show each 'point' in the span of one page?"
Dunno if that helps, but it's actually how I write my scripts-- I write a couple sentences/a short paragraph about ONE important thing that happens per page. Might be worth a shot.