Kathryn blogged this here a while ago – and I get the impression that it can be fixed if you can get the attention of somone from twitter. Solobasssteve told me that he managed to get through the unresponsive support system and his tweets are now being picked up.
Update: 29.7.09 – it worked! The search is now indexing my hashtags! Ppl power! Thanks to http://www.twitter.com/charles for fixing this for me.