The first ID contains brackets and a trailing slash while the second does not. Alternatively if the engine is opened with a .uproject argument no ID will be created until the "Open Project" dialog is opened. In the latter case one ID will be written, if the dialog is closed and reopened the second will appear.
Results: An Install.ini file is created with multiple IDs to the same engine.
Expected: Install.ini should have one ID per engine.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-99862 in the post.