Another set of plugin related files that can cause issues (although this one is not down to anybody as a fault) are these:
(you will have one or the other of these, depending on version of Cubendo installed - the v2 file is for C7/N6, the other is for earlier versions).
Deleting this will force a rescan of all 3rd party plugins installed except those on the blacklist. This seems extreme, but can be very helpful if you use Waves Mercury
, where they are continually updating/improving etc and a rescan will eliminate all references to plugins that are no longer there.
Defaults.XML is another file that can get corrupted.
This is just my opinion, but I think that what sometimes happens if you allow settings from earlier versions to be ported causes conflicts. For this reason, I usually make sure that a new installation cannot see older settings. The easiest way to do this is to create a folder in C:/Users/<username>/AppData/Roaming/Steinberg/<CubendoX>/ called "Backup settings" or something, and move every earlier version's settings into this - just drag the folders into it. A new install will no longer see them and will build a brand new set of default prefs and then you can simply move the old ones back again. (this obviously only works with an installation of say C7 where you previously had C6.5 or similar)