Alright, I stopped complaining and started work at solving this problem. I created https://issues.apache.org/jira/browse/OPENJPA-2296 and I started debugging the issue with the Eclipse debugger to localize the problem.
I suspect that the bug is inside JDBCStoreManager.createEagerSelects(). This is the method that determines the list of Eager relations that is shown in the trace. When Project - Employee is toOne it does consider Employee.projects but somehow skips it. One theory I have is that it thinks this relation is a toOne relation as well, but of course this is a toMany. When Company - Employee is toMany, this same code does not skip the relation and adds it as eager. I think at a high level in the EagerResultList we then see the consequence: the project relations are not yet fetched inside the "main query" of ResultObjectProvider.open(). After this, the while loop of EagerResultList adds entities and each call to load an Employee entity has to do an actual database load instead of reusing the entities that should be present in the context. I think someone more familiar with JDBCStoreManager now already has good directions of finding and fixing the problem and perhaps with the consequences of a fix. I will try and debug some more and add my results as comments to OPENJPA-2296.
