Not sure if this is a Linux problem. I have built a dual boot system Mint 18.1 and Windows 7 Pro (have to have the Windows as sat-nav updates won't work on Linux basic or Wine). If I re-boot from Linux to Win7 the mouse and keyboard don't work (don't know if there are other problems as I can't log on!). If I boot Win7 from a powered-down machine all is well.
Are there some checks I can do on the Linux install? Linux is installed on a Samsung SSD and Win7 on a hard drive.