I'm having an issue where my keyboard and mouse always work fine in BIOS/Grub/Windows loader/Ubuntu, but not Windows 7. I have legacy USB enabled, and XHCI+EHCI hand-off disabled. I tried switching to Windows boot loader thinking it was something with Grub, but the problem persists. I have googled and googled, but have yet to find a solution.
Sometimes a power cycle will get the keyboard+mouse working. The only way I can get it to ALWAYS work in Win7 is if I toggle EHCI hand-off in the BIOS (if it's enabled, I disable it, and vice versa). Once I do that everything is fine until I boot back into Ubuntu, then try to get back into Windows.
I have a cheap little MSI B85 board on this PC, not many options in the BIOS.
Maybe the Gods are telling me I should ditch Windows on this PC and use only Linux.
Actually, you aren't the only one. I get really screwy things happening to mine, but not anymore. I must have changed something at one point to fix it.
I would recommend moving the mouse and keyboard to different ports. It may have to do with fast boot (setting in BIOS and Windows 8+), it may have to do with legacy mode, it may have to do with something else too, but it's probably Windows drivers.
I had stuttering audio on mine whenever I pressed a key on my keyboard. Moved them around and the problem went away.