If you expand Characters, in the top pane.
And then click on a character name.

It should list the Battle.Net account in one field.
And the sub-account in another.
First check that that is listed correctly.

Also make sure that each character is being loaded in the correct slot.

For the file virtualization...
I'll assume you are virtualizing Config.WTF as something like Server-Character-Config.WTF.

When I make a new team, it initially does not remember which account is in which slot.
I have to enter the correct account name the first time.
And then check the box to remember the account name.
Once that has been done, the virtualized (per character) stuff is set to remember that account name.
So check that the box to remember account name is enabled/checked for each warcraft slot.

Beyond that, if none of those fix it.
Contact Lax.