Thanks for the update. We've been carrying out some further tests in-house, but unfortunately haven't been able to reproduce the behaviour you reported in your first workspace. It's certainly a strange one, and is still on our radar, so we'll continue to investigate this and will update the thread with our findings.
I'm experiencing the same issue with unlocked packaged apps not showing up in Application Builder. This has occurred immediately after upgrading this instance from 4.1.1.00.23.
Application Express 4.2.0.00.27
Oracle Database 11g Enterprise Edition Release 220.127.116.11.0 - 64bit Production
Oracle HTTP Server 10.1.3.3.0
Enterprise Linux Enterprise Linux Server release 5.4
Any further information you need?
(This is all on a VMware Fusion 5 virtual machine: you can have the VM if it would be useful and we can figure out how to get the 26GB .vmw file to you...)