Situation: Agents on WinXP SP3, updated cleanly from ZCM 3.0a to 3.1, no previous problems of slow logins, User source is campus AD.

For these workstations, after a reboot (or power on in the morning), time elapsed between entering the password and having a usable desktop became from 2 to 20 minutes, averaging about 10 minutes.
During that time the workstation was unresponsive and had simply the background image.

After it finally finished, everything seemed to work fine.

Setting this registry key
\HKEY_LOCAL_MACHINE\Software\Novell\ZCM]\ZENLoginUserRefreshAsync = "TRUE"

reduced the dead time to less than 1 minute. (Note this warning about the setting from ZCM Docs:
> IMPORTANT:If you change the login process to execute the device refresh asynchronously,
> the latest policies might not be immediately available. With this setting, the choice
> is login performance over the accuracy of the policies.

This may be old news to most people, but it was not to me, nor the Novell first level support tech.
Still don't know why it started being so slow only after the update to 3.1. No problems in the install or in configuration or log files was identified.

Newer machines with Windows 7 suffered a similar slowdown, but much less severe.