We had a ticket open (Ticket# 2584706) about this. Here was the determination as to what was happening.
"... it has come to light that there is a bug in cPanel which is likely responsible for this. The bug causes the rebuild_sprites (responsible for theme images) script to ignore reseller branding and revert to the root branding. As the rebuild_sprite script is run each night as part of the update check, unfortunately that means the only workaround for now is to disable automatic updates. After that, a reseller can go to the branding editor in WHM, and click the rebuild sprites button there. That should properly update the branding with their own logos again, and with automatic update disabled, it should stay that way. You will want to keep an eye out, as a proper fix for this should be made available with the release of 11.32.3.x of cPanel/WHM. Once that (or a newer) version is released, you'll want to reenable updates, or update manually and ensure that the branding is still being maintained."