Line 62 in /skins/_atom/_main.php should be changed from:

<link rel="self" type="text/html" href="<?php $Blog->disp( 'atom_url', 'xmlattr' ) ?>" />

<link rel="alternate" type="text/html" href="<?php $Blog->disp( 'atom_url', 'xmlattr' ) ?>" />

Proof is here:
http://feedvalidator.org/check.cgi?url=http://blogs.balupton.nghosting.info/index.php?tempskin%3D_atom

line 4, column 108: "self" link references a non-Atom representation [help]

... osting.info/index.php?tempskin=_atom" />

Message

"self" link references a non-Atom representation.
Explanation

This often occurs when people confuse "self" for "alternate".

From RFC 4287, section 4.2.7.2 (emphasis added)

1. The value "alternate" signifies that the IRI in the value of the href attribute identifies an alternate version of the resource described by the containing element.

3. The value "self" signifies that the IRI in the value of the href attribute identifies a resource equivalent to the containing element.

Solution

Generally, this problem can be solved by changing the rel value on the link from "self" to "alternate"

Heres the url for the demo site that actually has 2 errors ;)
http://feedvalidator.org/check.cgi?url=http%3A%2F%2Fdemo.b2evolution.net%2FHEAD.php4%2Fblogs%2Findex.php%3Fblog%3D3%26tempskin%3D_atom