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A bug appears, however, when I /disconnect and reconnect with the blank /server command. Eg, Instead of reconnecting to znc-efnet, it will connect to znc-freenode by sending the wrong server entry's password (this password instructs znc which network to connect to).

This is by design. When you type /server, mIRC will connect to the most recently connected server address (the one shown in the status window titlebar). It has worked this way ever since the /server command was created. If you would like it to connect to the server group name, you will either need to type /server group, or set up an alias that changes the default behaviour of /server to connect to a group name instead of a server address.

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Resolution of this will require some new way to distinguish server entries besides solely on their IP/Host.

As Loki mentioned, this has been previously discussed and one idea was to use the server password as a distinguisher, although that too is not ideal in cases where the same password is used for multiple entries, so it doesn't seem like a practical solution.