I was able to work around this by pasting in the path to my rvm ruby 1.9 to flymake-ruby-init in starter-kit-ruby.el
I'd love to know a better solution, though.
It could be that you're hitting the OS X bug that ignores your .profile for all applications launched from the GUI. But really I'm not sure; I haven't used Ruby in a few years. I could use some help maintaining the Ruby support in the Starter Kit; I'm not really qualified to do so any more.