For some screwed up reason, Macromedia invented an new object hierachy for fills. Objects can be filled and Groups can be filled, but one overides the other. To avoid this problem do NOT select and change groups using the solid arrow tool. Instead, select the objects with the Halo Arrow tool (or Option Click and Drag). This selects the objects and not the groups. Now change the object fills accordingly.

I have been using FreeHand since v1 through MX. Macromedia's best version of FreeHand was version 9. Since then, they have repeated messed up this program in a such a way, I have very difficult time convincing Illustrator users to use FreeHand MX.