In ST6 update 10 we have an assembly where the mate shows a zero offset but the part is shifted out by a small amount. I looked at the Update Relationship button but it is grayed out. I turned off automatic updates but it is still grayed out. I swear it seems like I have ran into this issue before but can't find anything on it in my IRs or on the solution database.
I have this problem too. I made adjustments to a part file, which (apparently) caused relationships to be conflicted, making the assembly misaligned. However, if I surpress then unsurpress any of the conflicted relationships, then it goes back to how it should be.