Importing simplest java project (in attachment) gets sometimes imported as "Java, JDT" and sometimes only as "Java". I am not able to provide exact steps to reproduce, as it seems to do that randomly.
Looking at http://git.eclipse.org/c/e4/org.eclipse.e4.ui.git/tree/bundles/org.eclipse.e4.ui.importer.java/plugin.xml, project should be detected as JDT, in case ".classpath" is found in the project. Couldn't be the issue the order of executing configurators? Like when Java configurator is called first, it creates .classpath and then JDT configurator is called and it sees the .classpath file. When the order is opposite, JDT is not configured, because .classpath is not there yet?