Something is wonky with twitter's search function. In May 2010 twitter search started returning results for keywords in the original, unshortened links passing through the service. Were http://example.com/booga to be shortened and tweeted, searches for "example" and "booga" would turn up the tweet.
At some point in late September 2010 this seems to have changed. Now the original URL is generally not matched, with the possible exceptions of Top Tweets, Promoted Tweets, and Twitter's own t.co shortener. The change seems to have ramped in slowly, as even three days ago I was seeing some shortened URLs turn up in search results, while others did not. There were also a couple examples of the host portion like example.com not being indexed, but the rest of the URL triggering search results. I thought it was a glitch, but as of 9/28 it seems consistent: URLs behind third party shorteners are not being indexed.
Its possible this is just a glitch due to traffic growth. It could be a normal adjustment to the Twitter service, attempting to tweak search results for better relevance. It could be a rather bold incentive to use Twitter's URL shortener. However I cannot help but notice that it also makes room for features relating to brand management. Searching for something specific might use the regular search service, while monitoring for all links pointing to a site could be a service from a different, premium system.
Update: Apparently its just me. Tweets sent from @dgentry containing shortened links do not appear in search results for keywords in the original URL, starting late September. For example, the following tweets did not appear in search results for codingrelic or geekhold: 1 2 3 4 5 6 7 8. I also noticed thiat this tweet did not appear in a search for "ifixit." I suspect that this affects any tweet I've sent since mid-September, but I didn't start checking all of them until I realized there was a problem.