I guess the issue comes from the ensime-sbt-project-dir-p function (in ensime-sbt.el) that looks for *.sbt or project/Build.scala files exclusively.
In fact, in my project, the sbt (0.12.2) build file was named project/my-project-build.scala, as the project structure had been generated with:
g8 typesafehub/scala-sbt
Changing the file name to the more standard Build.scala solved the problem. However, it would great to support any *.scala sbt project file names.
I may try to fix this and propose a pull request.
Happy hacking with ensime.