This sounds like the kext that controls the built in keyboard / mouse is either missing or damaged. I believe the kext in question is something along the lines of "IOUSBFamily.kext". I doubt this would be a hardware/firmware issue though since Windows recognizes input from the built in keyboard/trackpad.
You might try repairing the disk using Disk Utility in the recovery volume and then repairing permissions using Disk Utility while booted to your Macintosh HD volume.
If those don't resolve the issue then I would attempt an archive & install of the OS...
- To boot to the recovery partition you need to power it off
- On start up, using the USB keyboard, press command + r or if that doesn't work press option until you see your partitions, then select recovery 10.x
- Wait for the recovery tool to boot
- Select "Reinstall OS X"
- Follow the on screen prompts to reinstall OS X
This process SHOULD preserve your data but as always it's a good idea to have a backup of any pertinent data beforehand. The reinstallation will go through and reinstall the base system files, which should include the missing/damage kext responsible for the problem, while leaving any files you've added alone.
Hopefully all goes smoothly and that fixes it for you!