I've seen this issue for quite some time now, on multiple PCs I use DOpus on. The common factor is that I'm recursing multiple folders, typically by selecting Flat View. It only happens (very roughly) 1 time in 100 that I use flat view.
When the message comes up, the application being "configured" (almost always MS Office) configures quickly (< 10 seconds) and everything seems fine. Sometimes, after it's happened, the next time I open an Office app, the "configuration" will happen again. Occasionally the configuration takes some time (more than 1 minute) and is frustrating, but I've just lived with it.
I've recently set up a new PC and have had some issues with Office because I need multiple versions of Office installed (thanks to MS for removing ADP support in Access 2013), after days of fiddling, I'd finally got Office stable.
Thus, when this 'configuration' prompt came up today while using DOpus flat view and broke my Office install (stopped Outlook working altogether), wasting a couple of hours in uninstalls/reinstalls, I've been prompted to report the problem this time.
I can't find any reference to this issue on these fora, apart from one ref to Messenger being configured - the solution of uninsllaing the app not being workable in this case.
It seems that something DOpus is doing when checking files in a folder is triggering this "configuration''. It'd be great if it can be fixed, or shown to NOT be DOpus causing this.
It won't be Opus causing it directly. Opus will just be asking Windows and your installed shell extensions for details like file icons, thumbnails or information to display in the columns you have turned on.
One of the Office shell extensions is probably getting involved in that process, and deciding that its installation is incomplete or in need of repair.
With multiple versions of Office, you may have a mixture of Office shell extension versions, and something triggering the extension for one version may make it want to repair the registry in a way which then makes the other version think the registry needs repairing. The two versions may be fighting with each other, overwriting the other's registry settings each time they are invoked.
Someone more expert in Office, and mixing different versions of Office on the same machine, may be able to offer advice on how to fix or avoid the problem. A forum more dedicated to Office is worth a shot.
One difference between Opus and Explorer is that Opus will still talk to column shell extension which use the old (and in many ways more useful) API from Windows XP and earlier, which Explorer dropped support for. That could mean that Opus is invoking shell extensions which Explorer is not. (It's also possible you may be able to trigger the same problem by doing a search in Explorer which displays the same files and the same column details as in your Opus flat view.) But the issue is still that the Office shell extension versions are fighting with each other.
You can use ShellExView to view the list of shell extensions on your machine. It might be worth a try to disable the Office ones, or those from all but one version of Office, to see if it stops happening (after one more repair has been performed, of course).
I wasn't clear in that the PC I'm experiencing the issue on a lot has multiple Office versions installed, however the other does not - it has Office 2007 ONLY. The other one does only have this problem quite occasionally and never to the extent of breaking my Office install, so your explanation does hold up though.
I'll look into ShellExView.