1) Open attached project and proceed to "SpringBug" scene.
2) Go into playmode.

Expected result: Crates should hang on the same height.
Actual result: Crate to the left hangs lower than crate to the right.

Note 1: Sphere on the left has Spring Joint2D added in the Editor thus distance parameter is calculated.
Note 2: Sphere on the right has Spring Joint2D added via Script and its distance parameter is automatically set to 1 instead of being calculated based on relative position of both objects as it happens in the Editor

Workaround: You can calculate and set distance after you add Spring Joint2D component.

Reproduced with: 5.3.2p1 5.4.0b3
Does not reproduce with: 5.2.4f1