If you do an OS-based reboot of your the computer and your log-in screen is laggy or displays errors, it’s probably because
kexec-tools are handling reboots. When compiling an RT kernel, you were prompted whether or not to let
kexec-tools handle reboots. You are advised in the installation instructions (and here) to not allow that.
kexec-tools utility normally is used to perform ‘warm reboots,’ which is when the computer reloads a kernel without fully shutting the system down. (In contrast, a cold reboot is when you fully shut down the computer, meaning that the machine fully stops and it begins to cool down.) The lag you experience is probably because kexec-tools is rebooting to a non-RT kernel. Your system is at that point should not be relied on for running real-time applications.
To temporarily fix this, fully shutdown the computer to do a cold reboot. To permanently fix it, disable kexec-tools from handling reboots:
Now, kexec-tools will no longer handle reboots, and your system reboot as one would expect.