I'm troubleshooting a Windows 11 desktop where the left mouse button only registers every few clicks. The problem has continued across three different mice, nearly every USB port, and a powered USB hub. It also happens in Safe Mode, so it doesn't appear to be caused by a normal startup application.
The strangest part is that changing Windows' primary mouse button from left to right makes both physical buttons work normally, including the original left button now acting as the secondary button. Once a click does register, holding the button works normally for dragging folders and other items.
So far, we've tried different mice and USB ports, disabling startup programs, Safe Mode, and removing/reinstalling the mouse drivers in Device Manager. The mouse is a standard plug-and-play model without macro software. What Windows setting, driver issue, or other problem could cause only the primary left-click action to be intermittently ignored?
3 Answers
Since it follows multiple mice and ports, I’d check Windows’ mouse settings first. Make sure ClickLock is disabled, then test the primary-button setting again. The fact that the physical left button works perfectly when assigned as the secondary button suggests the USB connection and mouse hardware are probably fine, while something is interfering with the primary-click action.
Most basic mice use Windows’ built-in HID driver, so reinstalling the mouse itself may not change anything. I’d remove any manufacturer utilities or remapping software, even if the mouse is mostly plug-and-play, and test with only the standard Windows driver. Also verify that no accessibility or button-filtering settings are enabled. If possible, testing the same account with a newly created Windows user profile could help determine whether the problem is tied to that user’s settings.
You could try removing the USB root hub and host controller entries in Device Manager, then rebooting so Windows reinstalls them. That checks for corruption below the individual mouse driver level. Since the issue also occurs in Safe Mode, a low-level driver or Windows input configuration is more plausible than a normal startup program.
I believe the USB entries in Device Manager were already removed and reinstalled, but it may be worth checking the root hubs and host controllers specifically rather than only the mouse entry.

That’s what makes this so confusing—the original left button works flawlessly as the secondary button, but becomes unreliable again when it’s set as the primary button.