Why does my PC run better when Task Manager is open?

Malware is still a possibility. Some malicious programs can reduce activity when monitoring tools are open, and clean scans do not rule everything out. That said, this behavior alone doesn't establish that the PC is infected.

Try a Microsoft Defender Offline scan from Windows Security, and make sure your security tools are updated first. If you find something suspicious, avoid signing into sensitive accounts on that PC until you've investigated it.

I'd collect a trace instead of relying on a live monitor. Windows Performance Recorder can capture CPU activity to a file that you can inspect afterward with Windows Performance Analyzer. Start a recording, close the monitoring apps, reproduce the slowdown, then stop the recording and look for processes using CPU during that period.

Also check whether the slowdown happens after a period of inactivity. Windows maintenance or another scheduled task might start when the system is idle and pause when you interact with it. A trace can help distinguish that from a process actively reacting to monitoring software.

Don't overlook the monitoring apps themselves. MSI Afterburner can interact with hardware settings, so check whether it applies a profile when it starts. Compare temperatures, clock speeds, and power settings with and without it running, especially if CPU usage doesn't explain all of the slowdown.

Try changing one thing at a time. Opening Task Manager and opening Afterburner may have different effects even if both seem to improve performance.