After upgrading to 3.2, some key system templates were missing from several of the older blogs that caused errors, specifically ‘Site Javascript’ and ‘Comment Pending Template’. These older blogs never had these templates, and choosing to refresh them at the individual blog level did not add them. And now you can’t add System templates manually as you once could.

Found the answer here. Refreshing templates in the System Overview will create new templates as needed.

Refreshing all templates on a weblog

Go to the Weblog listing screen in the System Overview. Select a weblog and choose “Refresh Template(s)” from the action bar dropdown. All of the templates in that weblog that match default templates will be copied to backups and refreshed with the new code and settings.

This is the preferred way to execute the plugin because it is the only way currently to refresh System plugins and will add crucial templates which did NOT exist in previous versions (e.g. the Site Javascript templates).

This log from refreshing Ted’s Blog shows the templates being created:

Processing templates for weblog ‘Ted’s Blog’

Refreshing template ‘Main Index’.

Refreshing template ‘Dynamic Site Bootstrapper’.

Refreshing template ‘RSD’.

Created template ‘Atom Index’. <——–

Created template 'RSS 2.0 Index'. <———

Refreshing template 'Master Archive Index'.

Refreshing template 'Comment Preview Template'.

Created template 'Comment Pending Template'. <——-

Refreshing template 'Comment Error Template'.

Refreshing template 'Uploaded Image Popup Template'.

Refreshing template 'Comment Listing Template'.

Refreshing template 'Dynamic Pages Error Template'.

Refreshing template 'Stylesheet'.

Refreshing template 'Date-Based Archive'.

Refreshing template 'Category Archive'.

Refreshing (with backup) template 'Individual Entry Archive'.

Refreshing template 'TrackBack Listing Template'.

Created template 'Site JavaScript'. <———