I'll stick with my method
This actually never left my mind. I knew there was something wrong with your scenery.cfg I only didn't see it immediately. But now I know ...
You do have an issue with your scenery.cfg but you just didn't notice it yet. Your layering is wrong ... that is why Scenery Manager is 'missing' your scenery entry #99. As you don't have a layer assigned to that entry in your cfg, Flight Simulator will look for the correct layer in your scenery.cfg but it will not find it. That is a flaw which can be solved by pressing renumber in Scenery Manager ...
I ran this little test in my own scenery.cfg: I renamed the layer for the first entry to number "3". In scenery manager it also shows up as number "3".
This proves that Scenery Manager will spot faults in your scenery.cfg which you didn't even see. And also it' comes in really handy when you need to include flatten or exclude switches ...

