Oh, lol.

Didn't I explain? The topmenu resource we used was a hacked one from 2.50, because the 3.02 ones were impossibly hard for us to crack.
So, the extra icons were added at the end of the 2.50 one and were re-linked to the places they should be. Without them, the space where the icon should be would just be blank.

This is also why the Keys icon has a different icon, and why the icons that weren't in 2.50 don't glow or have shadows, like RSS for example.

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