When I log in, the system says it needs a reboot
Well, then reboot as soon as conveniently possible.
This message is usually due to a kernel upgrade having taken place. From Lucid on, the packages on LWP's are upgraded automatically, and this goes for the kernel too. When a new kernel is available, new modules are as well, and the system may try to load new modules into the old kernel, which may go wrong. Although sometimes a system can continue with new modules and an old kernel for months, it is usually a good idea to reboot.
We don't want to schedule this though, as a user may be running lengthy simulations or have other reasons to keep the system running. Thus we leave the decision to the user.