All of a sudden, when I try to use the ProChannel EQ, I'm getting this message... "You are currently using the Sonitus:fx EQ on this channel. To upgrade to the new ProChannel EQ, discard the Sonitus:fx EQ by Control + click on this button." But I'm not using Sonitus:fx EQ on that channel, and I was just using it yesterday... I did the latest upgrade, but that was this morning after discovering the problem, and the upgrade didn't help... any thoughts, it's really holding up my work.

SONAR projects created with SONAR 4 through SONAR 8.5 had per-track EQ using the Sonitus EQ. Opening these projects in X1 and newer throw the message described. See "Loading legacy projects" here http://www.cakewalk.com/Documentation?product=SONAR%20X3&language=3&help=ProChannel.02.html
 
 

This is for the any thoughts question of your opening post ....
I have gotten that message myself ....
When it does happen over here for me , it is because I'm opening a project up in SPlat that I had created in a version of SONAR that does not have the Pro Channel .The Sonitus  EQ appears to have been the default EQ in those versions of SONAR  
Typically happens when ever I revisit projects I have stored on an external HD that I have always wanted to finish ...
 
Are you opening a project that was created in a version of SONAR that did not include the Pro Channel ?
Or is this happening when you start/ open  a fresh project in your updated version of SONAR ?
 
In any event , when it happens to me I just switch over to the Pro Channel EQ section ..
 
not sure if I helped you , but hey I tried ....
The SONAR Calvary has probably seen the smoke signal and they are on their way  ..
I  always marvel at how scook can always provide the answer in one sentence or 2 at the most ...
 
Edit scook got me again , he posted the answer  while I was writing my post 
 
Kenny