Yeah, running as admin may be the key. Might need to work the IK issues with IK tech support. They are no stranger to getting their software working in SONAR.
Using the "Default All Plug-ins" layout.
VST3 plug-ins have an option where you are specifying the layout to origanize VST3 plug-ins by category. Most vendors add category information to their plug-ins. If the vendor fails to add category information, the plug-in will be at the VST3 top level. I have never disabled this option but would expect if the option is disable, the layout would work like VST2.
VST2 plug-ins are organized by the directory tree the dlls are found in. The dlls are the top level of the VST paths will be shown in the VST list top level. Dlls in subdirectories are listed in submenus. If you have enough VST2 plug-ins there should be arrows at the top and bottom of the list to scroll through them.
DirectX should be origanized by vendor.
If this was an upgrade did you perform this task
http://www.cakewalk.com/Support/Knowledge-Base/2007013315/SONAR-X3-Full-VST-Rescan-Recommended-for-Upgraders after upgrading. It should only need to be done once but could not hurt to do again.
Out of curiosity what is your plug-in count? I ask because I have seen very large counts sometimes not build complete lists if the background scan is running while opening a project. SONAR will occasionally issue a waring message about it.