The appearance of the logo in this area would be norml, when
/autoLogo=true, as the layout WinBoard uses in this case is like below:
What is strange, is that you have no clocks. You could try to set /autoLogo=false (in the ICC.ini file), which would display the clocks in the traditional way, as a single line over the full width of the window. But I woud be surprised if that would make the clocks appear if they were not displayed at all with logos. More likely is that you somehow have a font probem, e.g. that the font used for displaying the clocks is not installed. Are you using the standard clockFont? Perhaps you can use the "Options -> Fonts..." menu dialog to see if selecting another font or font size would help. What boardSize are you using (as ticked in the "Options -> Board..." dialog)?