From Paladin Software:
Most of the time Adobe InDesign 2.0 remembers where the tool palettes on your screen were positioned when last you ran the program. The next time you start InDesign it places those palettes in the same positions. However, sometimes InDesign appears to totally forget where your palettes were and put them in default locations. In particular, this happens whenever you add or delete a plug-in.
Palette Protector is a plug-in for InDesign, developed by Paladin Software, which fixes this problem. Palette Protector attempts to remember the positions of your palettes and put them in the right places. Iâ??m quite sure that sometime very soon Adobe will resolve this annoying idiosyncrasy, but in the mean time Palette Protector can help!