After upgrading from 3.0.1 to build 804 (for the new JUnit stuff) I've noticed that compiling when multiple output paths is enabled has become very flakey. Just to get it out of the way: yes, all my sources are in my probject. Everything worked fine before the upgrade, and now I can't quite figure out when the compile will take place and when it won't. If I switch to single output path, it works just fine.
It's strange, it tries to compile (it DOES compile I believe), but the class files never show up in my build directories. Anyone else experienced this? A coworker of mine had a similar problem with 3.0.1 just a couple days ago, so it may not be a problem only with 804.