If you kill a process via task manager you risk corrupting data (e.g. if it was half-way through writing a config file when you killed it, or if it just had not written the new file out yet). You should only ever do that as a last resort.
If you want to exit Opus, use File > Exit Directory Opus.
Try closing it in the proper way and see if the problem still happens. If it does still happen even then, then something may be blocking it from updating config files in your user profile directory.
Type /dopusdata into the Opus location field and push return. There should be a file called userdata.omd where you now are.
When was userdata.omd last modified?
If you view the file, what values does it have for last_version_low and last_version_high?
If you open userdata.omd in Notepad, are you able to save changes to it? For example, change the last_version_low number to 3, save the file, then exit Notepad and open the file again in a new instance of Notepad. Was the change saved or has the file gone back to how it was?
The .tmp file should not exist and suggests there may be a problem replacing the file. Try deleting that .tmp file.
Some users have found some Windows Store apps, including f.lux which is quite popular, block other software from updating their files. (We have absolutely no idea why they get involved or do this, if it's true.)
We'll also add an error message during startup if Opus detects this problem, so people know something is wrong.
If f.lux is blocking Opus from updating its config files then you'll run into the same problem next update, and may also find other settings cannot be saved properly, in both Opus and (potentially) other programs.
It should be reported to the f.lux devs, who may need you to give them more information about your machine or run some tests (which is why we can't do it ourselves).