If you find something you think may be a bug, it is best to post it on the AnswerHub. We are able to track issues better there while we investigate them.
I made an attempt to reproduce the issue that you described, but was unable to see the same results. Everything within the StarterContent folder appeared the first time the project opened after it was created. Are you using the binary version of the Engine that is installed by the Launcher, or did you build the Engine from source code? Does this only happen when creating a new project with one specific template, or does it happen regardless of which template you use? Would you be able to create a new project so that this issue occurs, then close the project and upload the log file from the Saved folder (don’t re-open the project)? Could you also provide your dxdiag information?