irc.alice.net uses 6667 and irc.bob.edu uses +6697
If you are able to reproduce this issue with a specific set of servers, I will need more information in order to try to reproduce this issue:
1) The full server entry for both of the addreses ie. description, address, port, group name, etc. so I can add them to an empty servers list.
2) The method you are using to connect to the servers ie. using the Servers dialog, or using /server group, or using /server address, etc.