Maybe you have more than one copy? I've had that happen inadvertently, after first letting the plug install at its default location and later re-installing it in a different location. Or you may have installed both 32- and 64-bit versions of the same plugin.
Look in the vst inventory in the registry. That's HKCU\Software\Cakewalk Music Software\SONAR Producer\Cakewalk VST\Inventory. See if your persistent plugins are listed there. If they are, the FullPath value will show the plugin's location so you can be sure you're deleting the right DLL.