Yesterday I found I am also experiencing the flat line eq issue in X3e. This can makes a huge difference in a mix and leaves one feeling like he's starting over.
 
I'm trying to complete this project so I don't know if it's happening with others or not yet....
 
Breath deep...

Sixfinger it states in your signature that you are running X3C, so please upgrade to X3E.
 
Then try a VST Reset. That is a reset followed by a rescan (not just a rescan) after you upgrade to X3E, if you have already, do the reset now.
 
http://www.cakewalk.com/Support/Knowledge-Base/2007013315/SONAR-X3-Full-VST-Rescan-Recommended-for-Upgraders
 
Cheers.

Six Finger...
For a while, when working on projects I care about, I was saving off the PCs so I could restore them if the Eqs went screwy.
 
Again, I haven't seen it since I got on X3, but I've not been working that hard on mixing either. My mixes have been pretty quick and basic. EQs simple and not spanning too many sessions.

Alex, I'll try that first thing in the morning, I am on X3e, at some point I know I did the VST reset, however, just a week ago I did and image restore and re updated to X3e from d.  I have great hope this is the answer.
 
Gswitz, when I first noticed I did save the the PC settings as presets on several tracks, oddly enough even loading them would'nt bring the eq settings back....   but I think Alex is right.  I've had years of no real issues other than some of the known bugs we've seen on these pages.
 
I'll rest easy tonight and reset both my brain and the VST

Sixfinger
Gswitz, when I first noticed I did save the the PC settings as presets on several tracks, oddly enough even loading them would'nt bring the eq settings back....  

Ok, that's a surprise to me. I've never saved PC Settings correctly and not had them restore correctly, including EQ settings. After you get on X3e see if you can replicate that one. That would be a big concern to me, because I do depend on that working as advertised.
 
It has never failed for me in my experience to save the PC settings and then reload. I use this feature rather heavily with my workflow. I often mix an entire night's music in one project. As I go through, I'll save the PC settings for each tune I mix. When I go back to a tune to make a tweak, I reload all the PCs and make my adjustments.
 
I would think I would have bumped into the bug if it were easy to reproduce.

I can happily say first thing I did the reset, and my aformention project loaded with EQ setting intact!
 
I will of course be watching closely.
 
Gswitz, additional info, yesterday when I loaded the project and discovered the flat line EQ's, I knew I had started with the preset Bus - Warm Concrete Drums, but had changed and replaced many things, however the EQ was the same. So I loaded that preset on a dummy track to visually compare the settings, Then saved the new drum PC preset.     
 
It was at that time when I reloaded the preset testing it , the EQ flat lined again.  Later after restarting Sonar and the project, the preset did work.....   I Really believe all is well on the PC presets, it was a moment in time.