Anthony,
Try including the gc.ParticipantVisit field in your custom query SQL. For custom queries to work with the time chart, both the ParticipantId and ParticipantVisit columns are required so that the time chart code knows how to join data between datasets/queries.

We tried to add a little bit of help text to this extent (see attached screenshot), but couldn't think of a great place to put this information.

-Cory