Did you remember to remove the INF drivers? Here's the process in more detail.
1. Plug in the DS3, and windows will install the dud drivers
2. Run the LibUSB INF Wizard, select the DS3, and install the INF drivers. Make note of the VID and PID, you'll need them later.
----- This is only done to get the LibUSB .sys files into the correct directories. You can copy paste, but this is easier and faster for me.
3. Uninstall the INF drivers using device manager.
----- Go ahead and checkmark "uninstall the driver" during the process. Or not, I'm pretty sure it doesn't matter. It doesn't remove the libusb0.sys files either way. Make note that if you are doing a FULL removal of libUSB you will need to delete them yourself.
4. Unplug and replug the controller. Windows will reinstall the dud drivers.
5. Run install-filter-win.exe, and install a filter driver for the dual shock 3, using the VID and PID you got before.
6. Now that a filter driver is active, native mode will be available in PCSX2. Run a game in PCSX2 and press the PS button to get the controller working, then set up the controls as you see fit.
Bonus - Once you get it working in PCSX2, the controller will work everywhere.