Only just started using Piwik (1.1.1) a few weeks ago and love it!
The working assumption is that this is related to the initial DB connection (using MySQL (4.1.12a-nt) on a Windows Server 2008).
Piwik is running on the same server so the embedded Piwik script code defines pkBaseURL by a relative URL as ‘…/piwik/’
(a fully qualified URL has the same delay problem)
We’ve also modified the hosts file to include the server/IP name
both hoping to minimize any DNS associated delays in the DB connection.
Looking for other configuration / optimization suggestions to minimize or eliminate that initial delay.