I think this is a display formatting thing more than anything else. I took your config and sample data and loaded it up. When I search on it, I do only see the time out to 3 decimals. I did a slightly different search, however, and found that Splunk is storing all 6 decimals, just truncating at display time.
If you run this search, you'll see the the results formatted as
5/11/11 1:51:16.192 AM 1305096676.192356
Which suggests that the time is being extracted/stored with full 6-decimal accuracy, but only being displayed with 3. I don't know the explanation for this behavior or if it can be changed - but it would be a good follow on question.