For AWS accounts accessed via CrossAccount Sign in, and all therefore using the same access key id and secret access key, when specifying the Account Type as Amazone S3(Credentials from AWS config or credential file), and config is specified, and the config file contains (an example entry):-
If i understood your question correctly you are referring to AWS Cross-Account Bucket Access, this is in fact a quite interesting question which we need to see from the software's side, so if you don't mind just send us the logs by navigating to Tools - Diagnostic, this will create a support ticket and generate all the info we need to check it from our side. Please reference this forum post in the description or mention Sergey N. Thank you.