I have the same problem, on occasion. The last time it happened, I had to restore a known good sessionrc to fix it. Luckily, I had posted one here on GC and was able to just copy it from the post and restore it. Here is the thread...
viewtopic.php?f=8&t=8092In that thread, Onkel Hatti referenced a know bug that is responsible for the problem. I suppose that you could use the sessionrc I posted but it will rearrange your docks to the way I had them. I guess you could put them back the way you like them. You can always make a copy of your current sessionrc (copy it to the desktop) and try the sessionrc I posted in that thread. If it doesn't work, you can copy yours back from the desktop and go from there.
You can also delete your sessionrc and GIMP will recreate it when it starts, That didn't work for me the last time this bug struck but it might work for you.