IE browsers always have problems because Microsoft refuses to abide by international web standards. Site and theme developers have to add specific styles for IE in order for their work to display correctly in those browsers. That means that a site could be perfectly well coded and show just fine in FF but break in IE.
In your case, NPRS, your theme, Greyzed, displays fine in IE9, so there must be smth you modified/changed that broke the layout.
In your case, Grisu, did you make any changes to those other themes you mentioned? Did you try viewing your site in IE9 see if it makes a difference?
Based on the location of NPRS problem, the issue could be due to a difference in the logo size, but it is really difficult to tell for sure.
I recommend that you backup your current theme with the modifications you made to it, delete it from wp-content/themes
, and reupload the original theme to see if the theme displays the way it is supposed to in IE. If it does, then you know what the issue is, and you simply need to identify where the “offending” code is located (as stated above).