I feel like a complete noob when it comes to MasterController. It's one of my favorite mods. But it's a bear to work with. *Snicker*
The only thing I can think of to may be fix the issue is to take away the step-brother/sister relationship status away from them. So they can be involved with each other.
Do you by any chance have a copy of the family you're trying to fix to maybe share with me? I could maybe use them to make some notes on how to tweak the relationship status. As right now all my current families I'm playing are all good relationship wise.
Edit to Add: I may have found a family I could use to make notes on tweaking the relationship status!!
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This may not exactly "fix" the step-sibling thing, but I'm hoping these notes will be good enough to help get an idea of how to fix the issue.
I used a 3-member family of Father, son and girlfriend. Made the father and son not related, and then related again.
Remove Family Relation:
Select the Sim > Left-click Nraas > MC. > Advanced > Family > Add or Remove said Sim.
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Add Family Relation:
Select the Sim > Left-click Nraas > MC. > Advanced > Family > Add child/parent/sibling > Active Family > Pick a Sim.
For status update select another sim and then re-select the other sim to check relationship status.
I'm adding a link to MasterController Cheats FAQ page, just in case it may help us both and others.
http://nraas.wikispaces.com/MasterController+FAQ