Well I think I solved a work around the problem.
It seems that an MDB in the system they had put some code
to set the jaas environment and call login on the module.
Removing this and using the unauthenticatedIdentity in the real module
allowed the cache cleanup to not affect anything. But I believe the cache
cleanup still shouldn't cause this to happen.
Wierd is that the session beans was using a different login domain.
And the mdb had the domain set explicitly to "other" which was different than the
session bean. The mdb did access the session bean which
it let be access because I think the run-as was set with the correct role.
Anyhow the cache did a logout and it somehow affected a client that was accessing a
session bean.
Code from mdb that was removed.
String userId = "test";
LoginContext lc= new LoginContext("other", callbackHandler);
lc.login();
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