I've asked moderators to merge these threads.
It appears you've excluded the leading cause of not getting MIDI notes from an external device to appear in a VI.
You also mentioned the thu preference settings, you normally don't need to do anything there. But since preferences get mentioned... make sure you try trashing prefs, just to be sure.
Another common issue is the wrong MIDI device selected in input, but the screenshots show you have "all" selected for MIDI input. I can't see anything wrong shown in any of the screen shots.
I am assuming you don't see any MIDI activity on the *MIDI meter* in the Instruments section of the mixer channel strip (not talking about the main audio meter on that channel strip) and along with no notes appearing on the track.
So I'm suspecting the problem is likely a MIDI one external to Pro Tools.
I don't think your Yamaha keyboard needs a MIDI driver to work, and I'd try uninstalling the driver and anything else from Yamaha. The "Emulated" indicates an old style pre-Windows DirectMusic thingy, I would hope (but have no real idea) it might goes away when you just reply on class compliance/no separate installed driver.
I would try:
Disconnect all MIDI devices, including any interfaces that have a MIDI section--except the MIDI keyboard you are trying to use.
Uninstall any Yamaha or other MIDI driver related software packages.
Reboot the PC
Make sure no other audio or MIDI apps or utilities are starting up and that you don't have any MIDI splitter or routing software, including stuff that might have been bundled with other software or hardware.
You can also install some MIDI monitoring software, like
http://www.midiox.com. And see if the key presses are at least getting to the monitor, and you can double check what MIDI device they are coming in on... and make sure that device shows up in Pro Tools.
DUC is so pathetic with how it downsamples images, it's better to post screenshots on a third party image sharing service and post links to that here.