Only one of the Selected Operations populates Index Analysis Grid and Histogram

Okay, just noticed that underneath the dropdown there is a label that is almost the same as the text in the dropdown except instead of having the Node number in brackets at the end it has the number of Indexes. Node 24 says one index and all the rest say zero. (The others are all relating to the subscriber-end of a replicated database and the default for replication is not to replicate non-clustered indexes.)

I guess there is a bit of a perception issue here - in SQL Server Management Studio if I expand out the Tables' Indexes branches it shows the Primary Key, e.g. PK_xyz (Clustered), but SQL Sentry Plan Explorer doesn't seem to "count" that one. Is it not a "real" index?

Actively investigating... can you verify what version of Plan Explorer you are using (Help > About)? This has to do with cross-database queries, and there is an active work item around this.