As Ramanjaneyulu said, I would check the routines. If you've reviewed the code and can't see any problem, you may want to try to remove any non-standard routine code and see if this is still happening (obviously backing up the code first).
A good practice here would be to load to a non-standard cube which is a copy of the original cube, plus any additional infoobjects you require. That way, you can load the original cube with the original transfer rules, and see if there are any differences between the records in the standard cube and the non-standard cube.