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You are right, this is broken in 6.4.1, a side-effect of a redesign of how the arguments of a command-line call to the notebook are parsed (the redesign was aimed at improving support for the ipython notebook in Sage).

Discussion on this sage-support thread reveals that after applying trac ticket #17439 you can run this command:

$ sage --notebook=sagenb "/home/username/mysagenotebook.sagenb"

Provided the fix in ticket #17439 is quickly reviewed, this should make it into one of the next Sage 6.5 betas, and be part of Sage 6.5 when it comes out.

You can read more about the recent changes to the parsing of arguments of command-line calls to the notebook on trac ticket #17280.