I will guess that she has not opted out and the CRA's sent alerts to creditors and an old collection or something popped up. All the new account activity would definitely cause a "trigger". I bet something popped up on TU that hasn't on EQ. They both should have dropped if it was from the AU accounts.
You should probably leave her on the accounts until the payments reflect anyway. One of the FICO scoring parameters is number of accounts with balances. So the paid accounts will drop that negative. If her score drops on the other report when the new accounts are added in then it is a simple matter to get them removed from her reports. But judging by the ages of the accounts you added her to and her own relatively new accounts it is not an AAoA issue.
If you find the need to drop them from her reports just call the individual creditors and request her AU status be terminated and then dispute the accounts with the credit bureau as "Not my account" and they will drop them. You may not want to drop them all at once. Take a look at which ones may be newer and drop them one at a time.
Also as has been suggested go over her report very carefully and make sure no new negative information has appeared between the two reports. That is a large difference without negative info. These were FICO reports from this site correct?? FAKO reports could have you both up in arms about false score changes.