Try replacing your preferences. Fast way which causes you to lose any customizations if it turns out not to be the problem is to hold down Ctrl + Alt + Shift , and while holding the keys down launch InDesign from the start menu or by right-clicking a desktop shortcut and selecting open (it won't work if you you hold the keys down before double-clicking a shortcut, but you can press them IMMEDIATELY after launching InDesign) and saying yes to the dialog asking if you want to delete your preferences. If you don't see the dialog, you weren't fast enough with the keyboard or you didn't hold the keys down long enough.
My preferred method, which saves your old prefs in case you want them back, is to close ID, open Explorer and make sure you are set to show hidden and system files, then navigate to (for CS and CS2) C:\Documents and Settings\<User Name>\Application Data\Adobe\InDesign\Version [no.] and rename the two preference files: InDesign Defaults and InDesign SavedData. In CS3 the SavedData file has been moved to \Documents and Settings\<User Name>\Local Settings\Application Data\Adobe\InDesign\Version 5.0\Caches. The preferences will be replaced with a fresh set of factory defaults when you relaunch ID, but if that doesn't solve your problem you can always go back to explorer and throw out the new set and name the old ones back again, restoring any customizations. If new prefs solve your problem you should delete the renamed files.
It's a good idea to also export any custom document and printer presets from the appropriate Preset > Define dialog prior to doing a preference replacement. Then you can just go back to the dialog and select load and you won't have to recreate all those wonderful things you've made and saved, and that will be wiped out with the old prefs files.
Once you have a customized set of preferences which work, make a copy and store it somewhere on your system for easy retrieval and you can simply replace the two files with your good copies when things get funny.