The mechanism seems to have changed.
Occasionally I have periods of masochism when I two-box. Mostly to run lower level characters through instances.
I have two separate folders installed and update them separately (except I did copy across after the MoP mega-update)
I used to be able to tick the "Remember account" box in each so that when I launched WoW I had the right accounts loading.
Now if I tick the box both remember the same account and if I re-enter the name for WoW launched from one folder it seems to carry to the other as well.
Have they switched to using a registry setting or something or in copying the folder did I inadvertently cross-link them?
Any advice would be welcome