There is some concern that reducing the min. token length to 2 will bloat the index and impact the performance of searching & indexing. While we investigate those issues,
the development version has been patched to change the min. token length for the index from a "magic number" to a define, http://dev.splitbrain.org/darcsweb/darcsweb.cgi?r=dokuwiki;a=commit;h=20081207161129-f07c6-6432947fe5d74666409d1e00222eaa489374c32f.gz
. This doesn't correct your issue, but it makes it simple to alter a wiki to use a different min. token length (e.g. 2).
The file involved, inc/indexer.php hasn't been changed since the last development release, so you should be safe to patch your copy in the same way. If you don't have darcs or patch the easiest way to make the change is probably to grab the latest nightly and replace your copy of inc/indexer.php with the inc/indexer.php in the nightly build. Once you have the change, you can add the following line into your dokuwiki configuration (the ideal place is conf/local.protected.php - if you use dokuwiki to amend your config settings).
Once you have applied the change you will need to reindex your wiki. For that you can use the searchindex plugin or have something spider your wiki (e.g. googlebot).
If you do intend to make this change, it would be handy if you made some notes prior to the change about your wiki (pages, total bytes in pages) and recorded before and after stats for size of data/index files & responsiveness of searches and reported them back here.