Same for me and my friend. Playing Cipher I have spent 18 points in INT and my spell effect cones and circles are base only. There is no outer circle representing the INT bonus. I tried making cipher with 3, 6, 10, 16 INT. The indicator remains exacly the same in all cases.
EDIT: After some testing I found that a wizard range indicators work properly (display both base and bonus range) but the actual effect of spells is limited to base indicator only.
EDIT2: This happens with 1.0.2.0508 verion of the game.