Eli Robillard has a blog item on this here
and he's given me permission to give the basic idea here.
Site Template Galleries and List Template Galleries aren’t upgraded during a migration.
One probability is that you already have created sites and lists (in v2) based on those templates and so they *have* been upgraded. The problem is that you have to find them and you also have to hope that they having been changed much since the site/list template was used.
That's a bit too risky so Eli before he upgrades a v2 installation first creates new sites and lists in that v2 installation from the templates. Those new sites/lists are naturally also included in the upgrade but you know where they are and that they haven't been changed since, so you can in v3 create V3 tempates from them.
Nice fix, Eli. (and thanks!)