I was having the same issue. One hint was that rbenv exec bundle exec command worked and that rbenv exec bundle install --path vendor/bundle worked, but their prefixed equivalents failed.
I wiped my ~/.rbenv, ~/.gem Gemfile.lock and vendor/bundle a few times trying to start fresh. Once these were cleaned away I tried the following:
rbenv install 1.9.3-p194
rbenv rehash # for paranoia's sake
rbenv global 1.9.3-p194
gem env # to check that everything was pointing at 1.9 and not the system
gem install --no-ri --no-rdoc bundler
rbenv rehash # necessary to load up the bundle executable
bundle --path=vendor/bundle
and it worked!
I think the important thing, since I tried this a few times, is to remove the .gem file from your home directory. It seems to get in the way.