I've some problem too.
I tried with two different account on two computer in my local network. Miranda is substantially the same (the last stable with the same plugins and nearly the same settings), only the MSN account changes.
The two contact's can't see online each other. Messages don't arrives. Both protocols are online, obviously.
I tried to delete and add again the contact in one of the two PC, and after I requested the authorization, it seems that the problem was solved. Unfortunately, the next time I connected the second Miranda, the problem was there again.
I tried the same with he first Miranda, the two contacts was able to see again each other, but I can't send messages (it timed out every time).
Then I put the first Miranda offline and then online, and it told me that the contact was removed from the server and asked me if I want to keep it as local contact.
This is my present situation!
EDIT: playing with the "stars" in the MSN server list I'm able to make the two contacts visible each other. Unfortunately it seems impossible to send messages. If I disconnect and reconnect the MSN protocol, again Miranda inform me that the contact has been removed from the server and ask me if I want to keep it as a local contact.