Doesn't sound too likely that its the OS as the changes are not as dramatic though its possible that the Preferences got corrupted in your lion update??
Once you reset the preferences in your user account you should be ok but it can also go corrupt if Indesign doesn't close them correctly causing corruption now when you reset them you would lose your customize menu setups and things of that nature.
One thing I would suggest would be to once you have your menus all setup make a copy of the preference to a location you can always copy them back from.
There are two ways to replace your preferences
1) There is a quick and easy method for doing this using the keyboard: close and relaunch InDesign, and IMMEDIATELY Cmd + Ctrl + Opt + Shift (Mac), and say you want to replace the preferences to the dialog asking if you really want to replace the preferences
2) The second way is to manually do it, now these files are hidden so you will need to set your system to show you hidden files.
Macintosh: Hard Drive/Users/<USER>/Library/Preferences/Adobe InDesign/<Version #>/<Language>/
Macintosh: Hard Drive/Users/Library/Caches/Adobe InDesign/<Version #>/<Language>/
This should fix the issue under your regular account.
Let me know if you need anything else.