I know it sounds strange, but.. ¿Do you use the ntpd service? ¿Is it active?
Yes, and yes.
It's the problem. I don't know why, but if the ntpd service is active and, in the boot process the network is unavailable you'll suffer this lack of time.
Making a definitive test is simple: deactive the ntpd service, take off the wireless NIC and reboot the system. If the next boot has the "normal" speed, you already know what is happens.
I wait you comments about.