I came here to ask a similar question, this time about the list of Customized Reports. I haven't noticed the issue you are asking about, but I will pay closer attention going forward with my nonprofit client.

But accessing the client through the Client's login vs accessing it through my Accountant Online portal show me a very different list of Customized Reports. Groups I create in one environment do not carry over to the other? I've gone back and marked every report Shared so, presumably, I can see all reports either way. I'm trying to get a consistent library of reports but this is very frustrating.