That is weird. Do you have the font size increased in your browser or anything like that?
You might try uploding
tmpl/cms/mininav.tmpl again, it's the template that seems to control the popup link for the Upload File page (from a quick check).
If that doesn't make any difference, I guess you could look at editing the link from within that file, this is the section of code you'd be looking for, I think:
CODE
<TMPL_IF NAME=CAN_UPLOAD>
<tr>
<td valign="top" ><a title="<MT_TRANS phrase="Upload File">" onmouseover="window.status='<MT_TRANS phrase="Upload File">'; return true" href="#" onClick="window.open('<TMPL_VAR NAME=SCRIPT_URL>?__mode=start_upload&blog_id=<TMPL_VAR NAME=BLOG_ID>', 'upload', 'width=400,height=400,resizable=yes')"><img alt="<MT_TRANS phrase="Upload File">" src="<TMPL_VAR NAME="STATIC_URI">images/lang-<TMPL_VAR NAME=LANGUAGE_TAG>/nav-upload.gif" width="95" height="32" border="0"></a></td>
</tr>
</TMPL_IF>
Hope that helps.