Just for the information of anyone who is interested,I’ve noticed my vaults seem to be indexed each time I restart too. The only difference is I only have a few dozen notes so far (not that experienced with MD yet xP), and it goes really fast. It never takes more than like 3-7 seconds.
However, there have been a few times where it seemed to become “stuck” during indexing, and just sits there. To fix this, I minimize the app and then maximize/restore it, and it seems to stop indexing and go straight to the vault. I’m not sure if anyone else has experienced this latter “issue”, but I thought I’d share, as it seems somewhat related to this post, I suppose. Good luck with your obviously frustrating issue. I wish I could help, but at present I’m too newbish to do so.