The Microsoft Windows Malicious Software Removal Tool doesn't detect all malwares and it only has list of well-known and dangerous malware and not the entire list of all malwares. Meaning, your system might have been infected with other malwares which are not in the list of this tools.
To scan for complete list of malwares, you have either use updated version of the Windows Defender or Safety Scanner which contains list of all malwares.
It is also assumption and something else might cause this issue but it worth a try to find out.
