I don't think the template is something you 'choose to use' - hopefully the WA guys will put me right on this, - but I think it's part of the solution (as it were) and is referenced/required by the WAUE_contact_1.php file.
I may be entirely wrong, but I [i[think[/i] that unless you have actually decided to remove it, it will still be on the server telling the sent universal email roughly what to look like.
Just to make sure, it may be worth opening the 'WA_Universal_Email/Templates/contactus.php
' file and specifying a background colour just to narrow things down a bit, and send it to the remote server.
If there is a problem with the recipients default email setting if a background colour is not specified, then that would rule out that possibility. It would perhaps have to recognise a specified background colour.
Oh right, - what Jason said.