If a pager is missing, then appears when using another theme, does that narrow the problem to the original theme?
I stumbled on tostinni's answer in Pager disappears when adding &quot;GROUP BY&quot; in the SQL query.


  Your query with the GROUP BY is incorrect, MySQL is lax enough to let you write this kind of queries but it is by no way recommended. When you use a GROUP BY clause you should group all the columns without a aggregate function.


I then fixed two queries that have poorly formed GROUP BYs, but my pager was still missing. I bust out Devel's query logging feature; the offending SQL query resulted to be used by the Nodequeue module. I checked the bug reports for that module, and found the one about that query: Grouping error" when creating a simple queue (PostgreSQL).