What makes you say it clearly isn't low? When you go to Settings / SD & phone storage what does it say is the available space under Internal phone storage? If that's below a certain threshold, (10 or 15MB I think) you'll get that warning. If you're basing your conclusion of clearly not being low just on the number of apps you have installed, your browser might be using up a good chunk of your storage with it's cache. I just freed up over 5MB and got rid of a low disc space message this morning by clearing out my browser's cache.
EDIT: Just freed up another 1MB by clearing the cache on the stock browser I don't use anymore since I installed Skyfire.