Ah, perhaps NI use the same driver for their virtual midi ports too, i know they use BOME software in the pipeline somewhere.
I’ve seen people complain that as NI use virtual ports, they could easily branch off the pads into their own MIDI port as an option for users who’d like to separate pads from the controls.
It’s a shame you had to uninstall it, though, because it really adds to the experience when pads are on their own port - plus it’s part of your original question lol. 
The other way you can filter them out is to use the input transformer on tracks where the pads will be used:-
Set it to global mode:-
Then pick the Pass Ch2 pre-set (Or Channel 15 in your case? Whatever the pads are on)
And only Channel 2 (15) items will make it through to that track.
Using the global mode you can just pick global for the other tracks and the same settings will be used.
That’s VST Instruments ‘Global’ mode (Page 43 of the remote control.pdf), it sounds as though you have a shift button held down somewhere - perhaps you have mapped parameter 83 to a button that is set to toggle/gate mode?
It should be as per “VST Instrument Settings - Selected Channel” on page 41.
That would explain why the channel selections were taking you to the end of parameter pages also.
One other thing to note is that you can re-order and re-name parameters using the remote control editor (See here)
I uploaded an example mapping for retrologue, if you want to try it - i have a load of mappings like this that i was going to upload somewhere so people can share setups. (Retrologue Remote Mapping)
But as it’s a little convoluted how to install them, I’m holding off until I get some time to make an app that will backup/copy them into the correct positions direct from the cloud. Cubase userbase seems so sparse in regards to community patches it needs a good kick!