Fixed it!
Went back to my original code, then started to remove the section above the copyright section, when I removed all but the CEOP image all was fine, added the links on the bottom right and it went out of alignment again.
I found by adding clear: both, to by definition of .copyright it fixed it.
.copyright {
background-color: #fff;
color: #001323; /* Scout Black */
font-size: 0.8em;
padding: 0px 0;
text-align:center;
margin: 0px;
clear: both;
}
Thanks again for all your help.