We frequently have this problem as well. It's always Experience A that has fewer visitors than the new experiences created, despite the traffic split being equal across the experiences. Right now I have a test with the following results in Analytics:
We have submitted various questions to Client Care about this and have not reached any resolution. Our only hope is that this will stop occurring when we migrate over to at.js and use A4T rather than our current mbox.js/Sc-Tnt integration.