Nick,
When you click on a feature, no popup appears?
What kind of feature layer is it? (point, lines, poly)
What kind of data? (Shape, GDB, SDE GDB, etc...)
How is it symbolized, what kind of symbol?
Is this in 3D, 2D or both?
I am just guessing that when you click on the feature the hit test for the feature, is somehow not working against the feature.
It generally works, so we should be able to figure out why it is not working in your case.
Mark