http://bugs.winehq.org/show_bug.cgi?id=28898
--- Comment #41 from William Pettersson william.pettersson+wine@gmail.com 2012-03-11 17:01:00 CDT --- Can you try running "Agent.exe" in a separate terminal, see if that makes it faster? I'm noticing that the whole patching process runs better when running it separately compared to just running the launcher.
For the record, Agent.exe (for me) lives in "~/.wined3/drive_c/users/Public/Application Data/Battle.net/Agent/Agent.649", and the 649 is the agent version so check what folders exist if/when any upgrade goes through.