After installing 64 bit Ubuntu 12.04 it takes over 3 minutes after login appears before the keyboard and mouse will operate
I had the same problem and I resolved surprisingly with http://paulphilippov.com/articles/how-to-fix-device-not-accepting-address-error
Not an answer, but I'm seeing similar symptoms. On startup my usb keyboard is typically not working well (misses the odd keystroke), but recovers fairly quickly. My mouse is much worse, and takes far more than the the 3 minutes the OP reported to come right, but if I try it later in the day its often working. It's a bit variable.
If I unplug my mouse and plug it back in, it works for a while (less than a minute) and then stops working again.
I'm using a Thinkpad x220. My impression is that thinkpads of various sorts are a common factor on related bugs posted in various places.
The built in keyboard and 'mouse' work fine.
Linux bug 990870, which paddington refers to does not match my symptoms. It's not a failure to register the device, which appears in lspci output as expected. Rather the device is not working properly.
Does this happen on USB or PS2 mouse and keyboard?
Are you able to use the keyboard if you remove and plug it back in within the 3 minutes of no response?
Have you tried 'dpkg --configure -a' and a 'dpkg-reconfigure -a' to see if this resolve the issue.
Have you checked the log files, like /var/log/dmesg?
A quick Google search showed similar issues and suggestions of a possible bug here https://bugs.launchpad.net/ubuntu/+source/linux/+bug/990870
This site might be helpful http://blog.neolocus.com/2012/04/ubuntu-12-04-lts-precise-pangolin-and-logitech-dinovo-keyboard-issue/ There are similar issues although not exactly the same.