so now when I insert a softsynth, it's input by default is "Omni", not my keyboard controller.  So now I am getting EVERY synth with MIDI-Out information playing onto new softsynths I insert into my project.
 
 

bumpedy bump

This is how it has always behaved for me.

it used to default to my MIDI controller only.

It has only ever defaulted to my designated controller if I use a project or track template, otherwise defaults to omni (though it was labelled "none") .

Same for me. It's always reverts to my MIDI ports because they are at the top of the list in MIDI devices.
Try moving your controller to the top of the list. Maybe this changed but this is how it used to work. 

From memory only midi outputs can be re-ordered under preferences. Midi input order can be changed in the ttseq.ini file.

I believe if you go to the Edits/MIDI Instruments in Preferences, you can pre-assign your Controller to Default, as well as configure the Output Port.  This particular Midi Preference is in serious need of updating though as it hasn't changed in probably 14 years.  The instrument definitions are old.  However, I believe the Default setting does not need to be configured, just assigned...