There are two issues with the header user icon.
1) When the header is a dark colour and the user hasn't added an avatar to their account, the user icon is barely visible.
2) The user avatar and the menu button in the header aren't aligned. About 3px out in Chrome.
A temporary fix is adding some CSS. If anyone is interested, this has worked for me:
.hub-app .hub-profile .avatar {margin-top: 3px; background-color: white;}