When the top navigation was moved into a VM in version 3.12 of JIRA, the HTML was changed slightly and now a blank link appears beneath the banner at the top of the screen. This is particularly annoying for customers who want a clean look and feel.

The relevant template is: \atlassian-jira\WEB-INF\classes\templates\plugins\topnavigation\topnav.vm

The line of code is:

<td valign="top" width="5%" nowrap>
<a href="${baseurl}/secure/Dashboard.jspa"><img class="logo" src="$jiraLogo" width="$jiraLogoWidth" height="$jiraLogoHeight" border="0" alt="$jiraTitle"></a>
</td>

Should be changed to:

<td valign="top" width="5%" nowrap><a href="${baseurl}/secure/Dashboard.jspa"><img class="logo" src="$jiraLogo" width="$jiraLogoWidth" height="$jiraLogoHeight" border="0" alt="$jiraTitle"></a></td>

i.e. the cell should be closed on the same line as the logo/banner, otherwise a blank line is added below.

I don't have a screenshot but let me know if this doesn't make sense.