Slow compiling on large project 132.839

We have a large swing client that we use to connect to a JBoss backend.  We normally compile the the server and client with ANT and this does not appear to have a problem. But developers compile and run the swing client in intellij and if I run the client, while another instance of the client is running, it always seems to use the incremental build and only takes a few seconds to compile.  If I run the client without another instance running, about 80% of the time the compile process takes about 10-15 minutes.  It is acting like it needs to comile all the classes again.  We use groovy as well so code stubbing is also done again. In previous versions of intellij this would happen if we used the external build.  We just disabeld that in 12, but with the EAP 13 I don't see an ability to disable it.

What would make it think it would need to recompile all the classes again?

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