I never tried, but maybe there is a hardcoded limit. Besides, a number of short words might be in stopword list.

 I'm not sure about your efforts to reduce minimum search term length to less than four characters but be aware that the built-in DNN search does NOT support substring searches.  That is, if you enabled 2-character search then a search for "DN" would not return results for "DNN" matches, only for exact matches to "DN".
 
Try it on this site:  A search for "DotNetNuk" only returns one result (thanks to a misspelling).  A search for "DotNetNuke" returns many pages of results.
 
I posted the tweak you need to enable substring searches here:
 
   TIP:  Enable substring search for DNN Search
   http://www.eguanasolutions.com/DNN_Blog/EntryID/38.aspx 

 
Another Option 
If the content you want to be searchable is publicly available (i.e., does not require login) then one free option is to replace DNNSearch with Google AJAX search as detailed here:  http://googleAJAXsearch.com  The free Google site search supports substring searches and it can provide search results from any document and/or PDF files you have directly linked, plus it's AJAX-based so results are returned in-page instead of in a new page.  You can perform multiple searches at once, tab through results without refreshing the page, etc.  A nice alternative for searching your site's public content.
 
-mamlin