Hi,
After fixing with malware bytes, you should have let it clean the entire drives. There is an option to select to scan entire system before normal reboot. Because, malware bytes normal scan run only in c: drive. I hope you understand.
Now, if you could start computer in safe mode, do this and then try to boot normal. Then if the problem is not fixed, then you could try to download JRT tools from bleeping computer.com or thisusu.org, and then run it. It will fix most of the third party attacks.
If those steps could not fix, then, it is better to boot in safe mode, download aswmbr from the avast site or reputed site and then run it on safe mode, and then wait. It will fix some hidden rootkit.
If it prompts to some corruption and asked you to run fixmbr, run it. You could safely run this command in that program. It will fix any master boot error.
Try and then post your progress