The number shown under one's name during chat, is the total rep (global) combined from all of StackExcahnge sites the user is a member of.  
  
[Here][1] is the link to MSO that confirms this for sure.  MSO is the mother of all metas and lets us know what is going on stack wide.  If it's something stack-wide (like chat) this is the definitive source.  Something specific to a particular site gets more attention on the individual site meta.  
  
[1]: http://meta.stackexchange.com/questions/108258/chat-shows-global-se-reputation-instead-of-site-rep