It would be fairly difficult for Opus to automatically preempt/correct every possible way that someone (or some other program) could mess around with their registry, and the standard ways of taking over the folder associations should already be undone by what Opus does already.
If you can work out any specific registry settings that Opus should change/remove to solve the problem then by all means let us here at the forum know (or let GPSoftware themselves know directly) but without access to your machine it's pure guesswork on this side.
I think the correct thing to do is get everything back to normal so that Explorer is the default -- i.e. undo everything that you did to make Xplorer2 the default -- and then tell Opus to take over.
If you want details of what Opus writes to the registry to take over the folder associations have a look at this FAQ. It's about manually undoing the settings but you can infer what they are from the descriptions of what to remote.
Oh, one possibility is a permissioning problem in your registry which is preventing the keys referencing Xplorer2 from being changed. Attempting to change them manually should answer that question (Vista/UAC issues aside).
There could also be a mismatch between what's in HKEY_LOCAL_MACHINE\Software\Classes and HKEY_CURRENT_USER\Software\Classes for the Folder filetype but that would seem odd as Opus writes to HKEY_CURRENT_USER which should take priority over HKEY_LOCAL_MACHINE. Still, there could be a strange combination of settings that I am not thinking of which is also not easy to see if you are looking at the merged view of the two Classes hierarchies under HKEY_CLASSES_ROOT.
There is an advanced option in Opus called global_explorer_replacement (type that into the Preferences filter box to find it quickly) which makes it write the registry settings to HKEY_LOCAL_MACHINE instead of HKEY_CURRENT_USER, and I think also uses a slightly different method for them, but I wouldn't recommend messing with this as it will probably only complicate things more than they already are. (Unless you have already messed around with that setting, in which case try turning it off.)
That's all I can think of at the moment. All I can do is guess without physically sitting down at your machine's registry.