By design, now the explanation...
Here the collision resolution is involved, every time you jump the collision system will "resolve" the player collision by push him enough to make him not to collide anymore.
Now, you're doing the same jump every time, but the position of the player's collision box changes a little bit every time too, but enough to even change the collision resolution result.
I want to make a little example, let's say we want to resolve a collision between two object by checking their collided pixels.
Here we have that the two object have collided 4 pixels vertically and 1 pixel horizzontally, it's more convenient for the collision system to push the player out by only 1 pixel horizzontally instead of 4 vertically.
I don't think the SFD engine uses pixel perfect collision checking but this example helps you understand that for the engine if I collide at 0.74267 in a direction and 0.74865 in another this will have a specific result even if you cannot notice the difference; can you imagine this applied even with linear velocity parameters in the collision resolution? And since SuperFighters Deluxe isn't deterministic, the same action (the same jump) would correspond to two slightly different results.
Off Topic
The window is about 21 pixels (2.5 tiles in height)