This is very true, and very frustrating. I've had to call all over the place trying to move flights around.
However!!!! I have found that some airlines don't check what is credited elsewhere. I've had my 5 IB flights credited for 10 total segments (5 on AY, 1 on CP, 2 on QF and 2 on CX). Five AY flights have increased to 7 segments. I didn't plan this, but they seem to go ahead and credit them anyway.