When entering runtime (Editor>Play) the prefab rotation offset, of 90' in this case, is ignored and causes the prefab to be offset by 90' at runtime.
This is my best guess at what the issues is, but definitely a regression causing my Generic Root Motion to be aligned down the X-axis, instead of the expected Z-axis forward direction.

repro:
- Import attached "Prefab_RM_bug.unitypackage" into a new Project
- Drop "CAVECRAWLER" prefab into scene
- Click the Editor Play button...
Bug: with the root selected, notice that the forward direction of the creature down the local X-axis, 90' off the expected orientation... use arrows to move.
see attached a7_BAD_Result.gif
Expected: the forward direction of the creature down the local Z-axis.
see attached a6_ExpectedResult.gif

this is a regression...
repro in...
Version 2018.3.0a7 (a7130d85cac7)
Not repro in...
Version 2018.3.0a6 (33e5def6e55f)