When a cape is applied to the player it will not be visually there on the player's back. This affects not only custom skins but also every other one.
Comments 2
Cleaning up old tickets: This ticket had been set to 'Awaiting Response', but has not received a response from the reporter (~3 months+) so is being closed as Incomplete. If you feel this is still a valid issue then please comment, or create a new ticket following the Issue Guidelines which includes steps to reproduce the problem.
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Do you use any addon or texture pack? This may be causing the problem