Greetings
Do you have the paid version of Malwarebytes' Anti-Malware installed? If so, this is normal for it to leave a startup entry present (a service) as well as a startup entry in the
Run key in the registry, but the entry in the registry doesn't actually cause the program to execute at boot time.
If you're using the free version then it could be a known issue with the current version of MBAM which can be fixed by running the appropriate version of the fix posted
here for your version of Windows.
Please let me know if it helped or not.
Thanks