It looks like you have this section in your custom CSS:
#header li {
padding: 0 !important;
}
.recent, .archive, .read, network, .tags, .memories, .userinfo {
padding: 10px;
}
#header .tags {
display: none;
}
#header .network {
display: none;
}


And now it should be:
#header .module-navlinks li {
padding: 10px;
}

.list-item-tags, .list-item-network {
display: none;
}

(I didn't intend to remove the old css classes on the header link items when I added classes to the list items, but apparently I did, and we have pushed a fix for that yet, so people can use their old code)