It's refreshing to know I am not the only one who has had the problem. Thanks for the links Aries, I will check them out. 

Anderton
For what it's worth...I just installed X3c (and set a system restore point first, just in case). I opened a project and it had a ton of missing plug-ins, including Cakewalk ones, which concerned me. I closed Sonar, opened, created a new project, and ran the VST scan. After the scan was done I opened up the original project, and all the plug-ins loaded properly.
 
Just to be ornery I rooted around my hard drive for some projects done in X1 and X2, and they all loaded properly too. This included several projects that had lots of plug-ins from Waves, Universal Audio, and other companies. So either I'm lucky, the Gods of Sonar like me, or the VST scan thing is indeed an important part of the update process.

That's been my experience also, Craig. I think the main problem (from what I've read and experienced myself) is there are certain plugins that may not have been tested with others at the same time. For example, I have several projects that use Pristine Space as my room sim for guitars along with a UAD 1176 crushing the room. I can't even open a project that uses this combination with the plugins turned on.
 
It baffled me that the project template containing these 2 plugs would even open. I come to find out the reason for that is both were disabled in the template. As soon as I turned them both on...bang! What's even more strange is, they can both be enabled in the same project. They just can't be on the same FX bin. So it is my belief that strange little anomalies like this may be some of the reasons we see crashes. Due to the plugin manager being new, we may experience a few growing pains.
 
I think (just my opinion here) this is what we may be seeing with some of the plugin issues. Another example....I have used ARC 1 version 1.1.1 for 100 years. I can't even open Sonar with that version. I've had issues with the later versions of ARC 1 not loading the corrections even though they are listed as "loaded". I have to reload each instance then the plug works. Using an older version stopped this...but Sonar X2 and 3 will not allow it without a crash.
 
Other than the above, I've not experienced any show-stoppers.
 
+100 on that reset and scan plugins advice, Craig. This is quite amazing as to how many issues it seems to fix. I don't think people are doing this correctly all the time. If anyone is not quite sure....here's how to do it just in case. You should do this each full install of Sonar from X2 to present and do it with each patch update.
 
Plugin Reset and Rescan:
Go to preferences VST. If your scanner is set to automatic...set it to manual just for now. (we'll put it back after)
 
Next, click the reset button. Unfortunately if you have any custom plug configurations, you'll need to put them back in...but this is a necessity.
 
Next, put checks in the box for both "rescan existing plugins" and "rescan failed plugins". Then press the scan button. It may take about 5-10 minutes for this depending on computer speed as well as the amount of plugins you have.
 
After it's done the scan, take both check marks out of the boxes marked "rescan existing plugins" and "rescan failed plugins" and set your scanner back to "automatic" if you want it that way. Close Sonar and reopen and this cures plugin issues completely about 95% of the time. If you still have an issue with plugs after this procedure, definitely contact support or fill out a bug report if possible.
 
I sure am sorry to hear about those experiencing show stoppers. I hate when that happens. I can remember a few versions of Sonar years ago that were like that for me. I couldn't wait to use them and heard from people how great they were because they didn't use Sonar the way I did....so I had to wait it out until a fix came. That's the other side of the coin....we use the thing so many different ways, it must be hard to track down some of these issues. Whew....what a nightmare that must be! Luckily huge fixes just about always come fast...let's hope the same thing happens here for those experiencing stuff like that.
 
-Danny

Seems like my problem was not as random as I thought then. I will be sticking with X3b for now. I use Sonar every day, all day, in the studio and whilst working on a new album I just can't have these kinds of disruptions in my work flow. I will keep an eye out for any other ideas to resolve the issues. Again, thanks for all the suggestions guys.

Danny Danzi
 
+100 on that reset and scan plugins advice, Craig. This is quite amazing as to how many issues it seems to fix. I don't think people are doing this correctly all the time. If anyone is not quite sure....here's how to do it just in case. You should do this each full install of Sonar from X2 to present and do it with each patch update.

Thanks Danny for elaborating on what I mentioned. I think a possible issue is that a full scan takes a looooong time if you have lots of plug-ins. So the first time you open X3c, you're able to work on projects while the scan is still going on in the background. This is why after opening Sonar and creating a project, I didn't do anything until the scan was complete.

I think it stopped sometime in X1's lifecycle, Colin.

Try this to see if it helps any (without doing anything to your plugins):
1) Uninstall Sonar X3c (or X3b, if that's what you have).
2) Run a registry cleaner (carefully) to clean out ONLY the Sonar remnants, not that this step absolutely needs to be followed.
3) Install X3a (the first copy you downloaded to install). Don't open X3a.
4) Now, upgrade directly to X3c.
5) Open X3c, double-check your Prefs and scan for your plug-ins.
 
From what I've seen, all projects should retain your plug-ins, and those plug-ins should be just as good as they were in X3b.
 
I would also caution to double-check that (in Preferences) that you do not have "Replace VST2 with VST3" checked, if you're using any VST2's when migrating your projects. Waves plug-ins are OK to be swapped out automatically, since X3b's release.
 
A considerable amount of testing was done for Waves plug-ins, with CLSID issues, and crashes for X3c. I have no issues now with Waves plug-ins in X3c unless I mix 32-bit with 64-bit, or VST2 with VST3's in the same FX Chain in ProChannel. I was one of the users more often able to have CLSID issues and crashes with Waves. Maybe this will help your projects survive the upgrade more seamlessly.
 
Lastly, IF this procedure helps, please let Cakewalk know. Maybe there is still an open issue moving directly from X3b to X3c that wasn't uncovered.
 
 

Thanks BRConflict. I might try that. I do have the VST2 to VST3 checked so that might be part of the problem I guess.