Duhh, found the problem:
Making the category ID available for use in the ad_ templates
If you have pages set for categories (ACP -> Options -> Node & Forum List) you may want to utilise the category ID in the ad_ templates, to prevent ad's being shown in certain categories for example.
To do so, edit the category_view template and add the following at the top:
HTML:
<xen:container var="$category.node_id">{$category.node_id}</xen:container>
That will ensure the category ID is available for use in the ad_ templates, allowing you to use the category node ID conditional as follows:
<xen:if is="{$category.node_id} != x">
This content will not show in category x
</xen:if>
Forgot to do that on the new style, my bad!