From the customer:
"I have everything setup in the Distribute menu. All certificates are correct, and I have my distribution provisioning profile selected which is different to my normal dev provisioning profile.
The issue is that Ti Studio isn't switching from using the Developer profile in XCode Code Signing, it instead is still using the Developer mode. So the issue is that it's trying to CodeSign in Developer mode into my Distribution provisioning profile so Apple gives you a Code Signing error on submission to the appstore."