Whenever you reboot or shutdown from the command line, you experience performance issues on your next session. Then, shutting down or rebooting by other means results in the machine behaving normally; or
At one point in time you shut down or reboot using the command line, and now constantly suffer a performance issue you cannot resolve; or
The issue is actually not related at all to rebooting the system, and you are just saying that rebooting the system is all you tried to do to resolve your performance issue?
The distinction is important. If it’s the first, I’m more likely to believe your interpretation of the situation. If it’s the second, there is likely a different issue you are not seeing. Possibly a configuration change or the installing of some sort of service that is now causing a problem, but whatever change didn’t take effect until you rebooted so you think it’s the command itself causing the problem.
If it is any of them, have you reviewed any logs on the system to see if there are any reported issues that explain the performance issue?