Ok, didn’t really want to ask this question as it should be quite a simple solution, but I’ve spent hours trying to resolve it to no avail. I have a web page with a text box, and then a select drop down next to each other. In Firefox and chrome they line up fine next to each other, but in IE the select box sits higher than the text box. Theres is no CSS applied to this select box, or the text box.
This is an aspx page, the generate HTML source for this is:
<label for='ctl00_main_primaryEmail' id='ctl00_main_primaryEmailLabel'>Primary Email: </label> <input name='ctl00$main$primaryEmail' type='text' id='ctl00_main_primaryEmail' /> <select name='ctl00$main$acceptedDomainsDropDownList' id='ctl00_main_acceptedDomainsDropDownList'> <option value='domain.com'>domain.com</option> <option value='doamin1.com'>domain1.com</option> <option value='domain2.com'>domain2.com</option> <option value='domain3.com'>domain3.com</option> </select>

It turns out this issue was CSS related. It was a border setting for the select element buried deep in the IE only stylesheet of the Blueprint Library, hence not showing up in firebug. For anyone else that comes across it, its this CSS for the select element