As referenced in this thread http://twittercounter.com/pages/help/reply/2273.
We're aware that our numbers differ from Twitter's at any given time. Please see below as to why that is.
Our records are snapshots of your account at any given time during the day. For example, we may have a snapshot of the account at night, and in the morning for the following day. This would then be different if you were to have snapshots of the account in the evening.
Furthermore, our graphs are displayed based on the EST (Chicago) time zone. This might explain why there would be small discrepancies for growth on any given day.