I have managed to successfully upload the app. The issues was that I was running OSX 10.7.5 and running Application Loader 2.8 (AL), which seems to be compatible with Moutain Lion (10.8). Once upgrading to Mountain Lion you can do another update to 10.8.5 which will install Application Loader 2.9. (You can upgrade to 10.8 via the Apple=>"App Store" option on your Mac. It is a paid upgrade.)
If you downloaded the latest AL from the itunes connect portal and install it, it doesn't tell you that it's incompatible with older verions of Mac OSX before 10.8. All you'll get is an obscure message that your ipa is an "unsupported architecture" which in "Appleonean" means "You need to upgrade your version of OSX". Extremely misleading as it's nothing to do with your IPA, it's your OS. Even reading the PDF from Apple about AL there is no indication for minimum system requirements..