Arm Switches, MIDI, and Other Strange Behavior

I have long had some strange behaviors with X1 and occassionaly with the V-Studio.  Here is a recent situation:
 
- When I created the project, for some bizarre reason, Fantom was set as my control surface.  I changed in back to V-Studio.
- Opened a new project with a few virtual instruments (2 instances of Kontakt, one RealGuitar, and one EastPlay-FabFour).  (I later added one instance of Vienna for an overdub but the problems started before that.)
- When I click ARM on a track, I see it armed on the Sonar screen and the master ARM light is red on the console, but the track's ARM light is not lit.
- I cannot arm a track with the track ARM switch on the console.  I have to use the screen.
- As happens from time to time in various projects, the inputs for the tracks change themselves.  For example, instead of Omni (which is my default for a soft synth), I will see Vienna or Console as the MIDI input.  (In other projects, sometimes the MIDI port I have selected as the input and/or output will randomly be set to some other incorrect value.)
 
Is there some overall thing you can think of--maybe a messed up Preferences setting or something--that is causing this?  I was able to complete the project--luckily it was a simple piece--but I don't want to fight these dumb problems all the time.
 
All thoughts would be welcome and appreciated.  Thanks. 

FreeFlyBertl, I appreciate it. I may wait on the upgrade for a couple of reasons--mainly that the tech and I are trying to isolate some things--but good suggestion. The odd thing is that some things like the Arm switch issue just suddenly occurred after a year of no similar problem.