I had Sonar X1 producer expanded and just updated to Sonar X3 (regular)
 
I did a screen capture of my VST folders in the VST plugin manager for X1 and matched them in Sonar x3.  
 
When I open up X3, only a handful of my plugins are showing up.  I've rescanned them etc but they are not displayed.  One that is displayed (EZdrummer) loads, but the samples wont.  
 
I open up Sonar X1 and everything comes up, Ezdrummer loads and the kits propagate. 
 
I installed the latest SonarX3 update. 

Unless you removed it, X1 Producer should still be installed on the machine. Did you reset and rescan http://www.cakewalk.com/S...reader.aspx/2007013315

Yes, the reset part is important too. Re-scanning isn't enough.

The EZ Drummer problem.
 
Is your X1 producer 32 bit and the X3 64 bit.
 
The 32 bit EZ Drummer will give the synptoms you discribe in 64 bit Sonar. You need to go to your Tooktrack account and download the latest version and install the 64 bit version.

I followed:
 
http://www.cakewalk.com/Support/kb/reader.aspx/2007013315
 
And still have the issue with missing plugins.  

Make sure to use the "Default - All Plug-ins" layout
Which plug-ins are missing?

Again, it would be good to know if your X1 was 32 bit and if your X3 is 64 bit, 32 bit DXi plugins will not work in 64 bit because that cannot be bridged by bitbridge.