The formatting should be back to normal - HOWEVER you have several options setable in your preferences - depending on these options if you display a message from the middle of a deeply replied to thread then that message may well appear over to the right of the page - my own settings are the default 'posted in last 2 weeks', threaded,single message + mixed order and this should be ok.
There is another setting in your browser that can alter the indent depth (normally set to about 5 spaces) but unless you have altered the accessibility settings that should not cause problems