For some of the images you have to edit some tpl files.
For the xcart.gif image you have to edit head.tpl
For the companylogo_small.jpg you have to edit:
skin1/mail/html/order_invoice.tpl
Code:
<TD valign="top">
[img]{$ImagesDir}/companyname_small.gif[/img]</TD>
Some tpl files have a dimension set, some not.