Using a material element with Apex cloth will override the morph targets so that they have no effect.
This issue didn't exist in 4.10 and seems to have been introduced in 4.11 due to the many optimizations made.
No changes occur in the skeletal mesh and the morph target isn't updated
The Cloth morphs and restarts the APEX simulation to accommodate this change. This behavior was present in 4.10 but broke in 4.11
Head over to the existing AnswerHub thread and let us know what's up.