The Eclipse compiler is different than the standard javac compiler especially when it comes to generics.
When having to maintain source code that was developed with Eclipse it can happen that the source code is not usable due to the different handling of generics. The only workaround is to use Eclipse for those projects. InteliJ for example allows to switch the project's compiler to use the one from the Eclipse platform.
NetBeans should support this as well. As the eclipse compiler can be integrated as an Ant task, this should not be a big problem as far as I can tell.