Ok, then you are using the same as me. I created a new game and SM-rushed the tech to have all it takes, then built a cruiser capable to launch huge two-staged missiles.
This is the MIRV
These are its parts:
Nothing on this is optimized in any way of course.
Here is the Cruiser detail:
Then I set up a shooting range, moved the guy into position and fired:
Separation range should be 150k before impact, and that is what happened:
It all works perfectly, so I am not sure what the problem could be. Small chance, but maybe you had pressed a time interval that was was too large? I guess in that case a mirv would just fraction earlier maybe.. not sure.
Otherwise - Mysterium.