I have a machine that is obviously infected, and when I ran MalwareBytes it told me that it found some "malicious" registry keys (surprisingly enough these contained file path to currently non-existent javascript files). But, that's it. Full scan did not uncover any malicious files, or malicious hidden processes in memory. Like, maybe the (hidden?) process that for whatever reason periodically injects keystrokes (hotkeys?) into whatever currently open window.

Then on another, not obviously infected, machine it found a "malware.trace" registry key but again no files or processes etc.

How does this jive with people's experience with MalwareBytes? Does it usually find registry key symptoms of an infection but nothing else? Or is it a common thing to have no infection but some malicious registry keys in place anyway?