Changing two publications at the same time causes deadlock in distribution database
It has been quite a while since I personally used replication, so I am not current on practical problems. A publisher with multiple subscribers is pretty common. However, Microsoft suggests using multiple Distribution databases when you have multiple Publishers.  The following post has direction: 

http://technet.microsoft.com/en-us/library/ms183524.aspx

"However, if multiple Publishers use a single Distributor, consider creating a distribution database for each Publisher. Doing so ensures that the data flowing through each distribution database is distinct."

It sounds like a recommendation to me.