I'm having the same problem!
Which generates this url and opens it in a new window: http://localhost/rep/Help/CSH/iSupportHelp.htm#<id=16>>wnd=SecondaryWindow
The new window then does more script processing and ends up with this url: http://localhost/rep/help/CSH/iSupportHelp.htm#<id=16%3E%3Ewnd%3DSecondaryWindow&t=Overvie w%2FiSupport_Overview.htm
It doesnt matter what mapId I pass in, I always get the default topic.
We just upgraded from RH10 to RH11 and we're trying to use the new responsive html5 output.
Are the map files selected in the Single Source Layout?
Also, Adobe released a fix for RoboHelp 11 that fixes issues with CSH for the Responsive HTML5 output. Please try the following fix: http://helpx.adobe.com/robohelp/kb/issues-in-robohelp-1103.html - It's not a patch, you will have to download it and apply it manually.