Is this a large table? Is one plan being stored in the cache with not optimal estimates?

Try clearing down the cache , updating statistics and rerunning or RECOMPILING

Yes , DDL and Exceution plans are useful.

Two potential problems:

1) rewrite to place as much information of the IN in the JOIN

2) consider the DISTINCT , and how...

Automation is good - up to a point . Many factors influence the SQL Server performance - the performance stack is from the query down to the LUN (or other...