To reproduce:
1. Open attached project "LineRendererEndColorBug.zip".
2. Play "Scene" scene.
3. Look at line renderers. Transparency looks identical on all line renderers.
4. Stop the scene.
5. In Hierarchy find "LineRenderers" gameObject, and for each child, uncheck "Start Transparent" in component "Change Renderer Colors (Script)".
6. Now play the scene, and see how differently it looks.

Expected result: Line Renderer's "startColor" and "endColor" is set correctly for "Color values", and "Alpha values".
Actual result: If Line Renderer has a different number of Color and Alpha sliders, then "endColor" will not set "Alpha values" to the last Alpha slider in the gradient.

Example:
If there are 2 Color, and 3 Alpha sliders, then endColor will modify 2nd Alpha slider in the LineRenderer's color gradient.
If there are 3 Color, and 2 Alpha sliders, since there's no 3rd Alpha slider, no alpha sliders will be modified.

Reproducible with: 5.5.0b3, 5.5.0p2, 5.6.0b3