Most of the time my tools don't show up over to the left (Layers, Links, Swatches, etc.) without me having to reset the preferences OR turning "Application Frame" on then off. This last being my new work-around. Now, turning off "Application Frame" crashes my indesign. The disappearing tools also effects Illustrator.
For more background, since upgrading to the last version of everything, when the tools disappear, selecting any from the "Window" drop-down, did nothing. Considering they work fine with Application Frames, it's weird.
Have you tried manually deleting the InDesign Defaults and InDesign SavedData files? (Not just used the keyboard shortcut?)