Acer laptop's built-in keyboard and mouse not working in Windows
Solution 1:
Had the same issue with my Acer Aspire notebook, of all things it turned out the battery was shot, once i removed it from the laptop the internal mouse and keyboard again worked normally.
Solution 2:
I have personally not heard of this.
If you are sure that it is working in the Linux installation it means that there are no faulty connections and it is a software based issue.
The best I can think of is that rather than the usual PS/2, the keyboard/mouse is being recognised as a USB based device and some how the USB drivers / root hub has become corrupt or an incorrect version installed.
If the external keyboard is USB, I am a bit further confused, but if it is PS/2, this may work to my theory.
The best I can think of is to use system restore or try to manually uninstall updates one by one.
Lastly, if all else fails, reinstall Windows and apply updates one by one until you reach the failure and you should identify where the problem lies.
I would personally start by going to device manager and uninstalling / removing (or rolling back) the driver for all USB root hubs and connectors then doinga plug and play scan which should reset/reinstall them. This may not solve the issue but should be a good start.