It is often dificult (a.k.a.) impossible to know why but sometimes you just gotta trust that the software knows best
I find the tip near the bottom of this webpage http://wikihelp.autodesk.com/Inventor/enu/2012/Hel
P.S. This note from the same wiki page can also be useful.
If the selected component is constrained relative to an underconstrained part, a cube appears on the degrees-of-freedom symbol. To highlight the relative part, hold the cursor over the cube until it changes color. The faces of adaptive parts which have degrees of freedom remaining are displayed in a contrasting color when you hold the cursor over the cube.
While these tips may not track down your exact problem they might help. Best of luck.