Do you have a lot of keywords in your meta settings for each page?
We may need to add a config option to not index those into the site search, it could possibly be causing this.
I don't think you should try to solve it, it has to be a code issue and something about your particular content I think.
For now maybe remove the SeachInput control from your layout.master if you want to hide the search temporarily until this is resolved.
Best,
Joe