[MrSmith]

Is there a way to get a line connecting two objects to render the whole way instead of stopping at the edge and leaving a space between the line and object?

[john.gersh]

That shouldn't happen, in general. How did you construct the diagram? For example, it appears that the clouds have magnets at their centers, which is not the default for shapes. One way to make your picture would be to group each cloud with a larger, borderless white shape behind it and move the line to the back. Might you have done that at some point?