We are just beginning to document our WebCT experience.
The most common login problem is from bookmarking the login page. This cause future logins to fail as WebCT checks the address used to invoke it. If that address is not "http://webct6.nmt.edu/" it will fail.
Most of the remaining login failures can be fixed by having the Help Desk (575 / 835-5437) set a new password. This can be done once user identity is established.
About the annoying pop-up windows about browser compatibility. We've not found a way to stop them or limit their number. Until we can upgrade our version of WebCT they will be with us.