I've had this issue for the past couple of versions of InDesign. I have a very specific tool panel layout that I like to use and I have it saved as a preference. My preferences of what panels I want and where are correct. But every time I close InDesign and reopen it the panels are all collapsed. They are the correct panels and in the correct place but I have to go and expand all of them to get them all open. This seems a bit trivial but it's a nuisance as I don't want to have to keep InDesign running 24/7 as I use this computer for other purposes (namely gaming). Anyone have any clues as to why this is happening? It's been going on for a couple years now and it's getting a bit old.
Here are some screenshots of exactly what I'm talking about:
Panels Collapsed (how they appear when I open InDesign and open a document)
Panels Open (How I would like them to appear every time I open InDesign.
Tool panel layouts are saved as Workspaces. But they could get corrupted if your InDesign preferences are bad.
Try restoring your InDesign preferences: