Vadim,
You wrote in the https://jira.jboss.org/browse/JBIDE-6541 issue that you tried it with "a clean workspace", but I asked you to clean the configuration (not the workspace itself)...
Did you tried to start eclipse with -clean option or to set osgi.clean option to "true"?
The trick is that something is cached in the workspace configuration for the Java Model, and since no Java code was changed the builder was not started at the first start of the new eclipse version. But eclipse (JBoss Tools and Seam Components model structure) was replaced with a new one, so actually the model needs to be re-build.
So, -clean option should help is this case. Did you tried it?