Hi Gareth,
I think I have some ideas about the issues being experienced. The issues I'm seeing are as follows:
This is how it would be expected to be seen, in Chrome: 
This is how it appears by default in IE9:
It seems that the header items are not floated correctly - I have fixed this to some extent by applying the IE9 float right fix detailed here: http://stackoverflow.com/questions/15665477/css-issue-with-ie9-and-floating-divs-aligning
This however only seems to work to separate the branding/courses and the user/messaging/gotobottom sections; it didn't seem to work to sort out the incorrectly ordered items on the right. I then had to manually set the background colour of navbar-inner, and override the strange filter settings back to initial.
Also, I manually overrode the background of blocks, and spaced the header of the main page block so it didn't overlap the dot image.
Here's the General CSS I've used to do this - I've got this to an acceptable state, in my opinion, and have tried to tidy up further in other areas but with no success. Unfortunately our client's standard Win7 build uses IE9, and our project doesn't carry enough clout to overcome the inertia of change for whatever reason.
/* ***************************
(Kind of) fix broken header
*************************** */
.custommenus {
width: 100%;
}
.custommenus .pull-right:before,
.custommenus .pull-right:after {
display:block;
content: " ";
}
.custommenus .pull-right:after {
clear: both;
}
.custommenus .pull-left:before,
.custommenus .pull-left:after {
display:block;
content: " ";
}
.custommenus .pull-left:after {
clear: both;
}
.navbar-inner {
padding: 0px 10px 0px 10px;
border: 0px;
min-height:40px;
background-color: #393;
background-repeat: initial;
border-radius: initial;
box-shadow: initial;
filter: initial;
}
/* **********************************
Put some space between breadcrumbs
********************************** */
.breadcrumb li {
padding-right: 10px;
}
/* *****************************
Fix content block backgrounds
***************************** */
section,
.block {
background-color: #fff;
}
/* *************************
Fix category combo header
appearing on top of the
dotted background
************************* */
#frontpage-category-combo {
padding: 20px 5px 5px 5px;
}
/* **************************
(Kind of) fix Awesome icon
lack of spacing
************************** */
#essentialnavbar i,
.header i,
.content i {
padding: 0px 4px 0px 4px;
}I also found the following link, from which you can download virtual machine images of Windows installs with older IE browsers. It's been really helpful, I've no idea if this is something that the rest of the world has known about for yonks, but thought I'd put it out there:
Although, in doing the images, I've just realised the logo is still missing ... 
More to do!
