The portable version would never write to the installed version's settings folder.
I suspect you weren't actually running the portable version when you did the settings import. You probably still had the installed version running in the background, and launching the portable dopus.exe just meant it noticed an instance of Opus was already running (the installed version) and told it to open a window.
Or maybe...
How long ago is ages ago?
It has only been physically possible to write a portable version of Opus to a HDD since Opus 10.0.1.6 beta, released in August (or Opus 10.0.2.0, released in September, if you haven't been installing the beta versions). That was when Opus gained the option to use a USB Flash Drive as a 'dongle', with the program itself stored on another drive. Before then you could only export the program itself to a USB drive.
Are we actually talking about a portable version that Opus itself exported (via Settings -> Backup and Restore -> Export to USB Flash Drive), or have you done something unsupported like manually copy the program files between drives/folders? (That won't work except on exported copies where the USB dongle option was used to create them.)
(I am assuming your C drive is a normal HDD, of course.)