Certain synths not responding - please help

This is a weird one. I have NI Komplete and certain instruments (Kontakt & Reaktor) aren't responding to my MIDi controllers. All of my MIDI ports are enabled. When I insert a simple instrument track, or manually add the synth and separate midi track, then choose my midi input, and click on the track, I don't see any metering like you normally get when you select a midi track and then hit some keys.
However, my MIDI icon located in the doc of windows, is showing a red light blinking AND in the instrument itself it's showing a blinking midi signal.
For example, in Kontakt I'll load an instrument and I know it's loaded properly because I can manually click the GUI keybed with my mouse and I'll hear the instrument play. But when I play my midi keyboard, which is selected as the input, I don't hear anything. There aren't any settings in Kontakt (VST version) to select your midi input, it goes by the host's channel selected.
I've never had this issue before in previous versions of sonar and other instruments such as Omnisphere load up without issue. I've tried other midi controllers hooked up to different midi ports as well. These controllers work without issue when choosing their inputs on a basic midi track for using external synths. I am going crazy trying to figure this out. Any help is greatly appreciated.

The issue has been occurring with my bass station II which I have tried both via USB and the standard midi port which is hooked up to a MOTU Midi Express XT on input port 2. I've tried both ways.

Whether using a midi track routed to the instrument or simple instrument track (tried both ways), my midi input is either "Bass station II", or "Motu input port 2", both set to omni.

Just to clarify, these same controller assignments work without a problem using Massive or FM8, which leads me to believe it has something to do with these specific NI instruments that work by loading sub-instruments, or whatever you call them.

Interestingly, to trouble shoot I also tried using these instruments in standalone mode and have had the same issue. However, they work fine when I have a different controller plugged into my RME Multiface's Midi in. So it seems this isn't a Sonar issue at all, but if you have any clue as to why this is happening or even a guess, it would help to hear from others.

I go to the synth rack, insert Kontakt as a simple instrument which Sonar creates the routing automatically for. Then in Kontakt I open a library and double click an instrument. Nothing special other than the ordinary is happening in this stage.

Like I said earlier, the weird thing is that the same thing happens when I open Kontakt in stand-alone mode. It's just my novation USB controller that isn't working. Also, like I said, it happens whether I choose the novation USB or use the 5 pin midi hooked up to my MOTU midi interface.

If I have a different controller plugged into the midi port on my audio interface (this is different from the MOTU), it works.

Kontakt standalone will even see the novation and I'll assign it to Port A but I get nothing. I think it might be some
kind of funky IRQ thing happening but it's just puzzling that it only happens in these "shell" instruments. The ones you have to physically load an instrument into to get sound (such as Reaktor & Kontakt).
I appreciate you trying to help but I think this might be a question for an NI tech expert.