with appload command do the lisp run as expected, load it and see if the command line appears some error msg.
Another hypothesis, maybe you have another command set with the same keys, and the last command to be loaded is the prevailing command.
Try to change the c:xxx in your lisp to a c:yyy that you have not defined to any other command.
hope that helps
Ive noticed this behavior in multiple versions (2010 thru 2013) then only time we can get the startup suite to work is if you're starting up using the icon, if you drag and drop, or double click to open this seems to bypass the startup suite. I recomend adding startup routines to the ACADDOC.LSP file.