The battle.net account functionality is not causing you're problems, I'll hop into different realms at the same time and then hop back to my main realm on all my accounts without issue. With the recent patch battle.net accounts did experience some log in issues, but I haven't had any outside of the publicly announced issues. Make sure to turn off any / all firewalls and try again? Sounds like something is prohibiting the 2nd WoW from fully connecting. If it is any server you try to connect both on, I'd imagine it's a firewall / software issue on your side, if it's just a specific server, could be a blizzard issue.