For me, the problem of running ScalaIDE and sbt ~ compile at the same time turned out to be the fact that both ScalaIDE and sbt used the same output directory to compile them. This meant that they overwrite each other with compiled classes and defined them as modified, which led to a new full recompilation instead of using incremental compilation.
To fix this, change the output directory of one of the compilers by doing one of the following:
ScalaIDE [project]/target/eclipse, project .
, , last compile sbt, ( sbt). , , . , sbt- ScalaIDE , .