It is a bug. See WordPress Trac Ticket#14883. If you change
#branding img {display:block;} to display:inline; it fixes the image being shifted right but does not fix the white space between the border.
Update:
The ticket still has not been accepted as a bug but a patch has been submitted.
Update
The patch has been accepted and the IE9 Header image display problem will be fixed in the next release.
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