Operating system: Windows 10 Enterprise, 64bit
Graphics card: Nvidia GeForce GTX 970
Broken: 2.80 beta, hash: c97c76c01c1d, date: 2019-01-04 00:26
Worked: 2.79b (official), hash: f4dc9f9d68b, date:2018-03-22 14:10
Short description of error
Incorrect results when apply "Clear Transform" on a bone hierarchy when Auto Keying enabled and Visual Keying enabled (Blender Preferences) or Visual transform Keying Sets are used.
Exact steps for others to reproduce the error
Based on the default startup.
Hide the Camera, the Light and the Cube (for better visibility).
Add Armature -> Single Bone.
Subdivide the bone once (so you've got two bones in a hierarchy).
Enable Auto Keyframing.
Enable "Automatic keyframe insertion using active Keying Set only" for Visual LocRotScale Keying Set.
Enable Visual Keying (Blender Preferences -> Editing -> Keyframing -> Visual Keying). Save Preferences.
Enable display axes of the Armature(for better visibility)
Transform the bones so that the pose is visually different from the Rest Pose.
Select the two bones and apply "Clear Transform" -> "All"
Use Tab key to check how the Rest Pose differs from the result of applying Clear Transform.
In 2.79 the result and the rest pose are identical(correct behavior). In 2.8 beta the result and rest pose are different(incorrect behavior).