Jar deployment omits classes

I am a mostly satisfied user of JDeveloper 9.0.3.1035. However I experience the following problem which seriously dampens my enthusiasm for working in the IDE.
Sometimes generation of JAR files from a JAR deployment profile omits classes. It does so silently, and in spite of the classes being checked in the deployment profile properties, and no compilation problems being present. So I don't see the problem until runtime, and it's not necessarily very evident what the problem is.
I noticed that it usually happens right after editing the java source of the class and then deploying the jar. The jar will be deployed as usual, but without the class in question. I have not been able to detect a pattern in which changes cause the problem to appear.
The only succes I have had in remedying the problem has been to delete the class entirely and create it again in the workspace. But sometimes even this is not enough and I seem to be unable to get the class included in the jar, even after removing and recreating both the class and the deployment profile. Needless to say it gets old after a while.
Has anyone else experienced the same problem, and possibly has a workaround for it? As it stands it is an unfortunate fly in the ointment in an otherwise very positive experience with JDeveloper.

Indeed the preview function shows me what is going to be in the jar (missing classes and everything). It does not contain any red lines, but then it doesn't contain my classes either, even though they are selected in the deployment profile gui, and all paths seem to be correct (several other classes in the same path are included).
I experience a complete mismatch between what is selected in the deployment profile interface, what goes in the *.deploy xml file and what actually gets included in the jar. After recreating the deployment profile everything is included. Then, if I go and uncheck some classes, the output is different, but not matching my changes (unchecked classes included and checked ones not included). Finally, in the *.deploy xml file, files are listed which are not checked and also don't get included in the jar (non-java files like jsps).
The runtime exception depends on the context, but it tracks down to the classes missing in the build (ClassNotFound etc.).

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