[AnotherCat]

If, as you say, Calibre is working ok I wouldn't worry about it. Windows 8 has a good reputation for sorting issues out for itself.

If it turns out that there is a continuing problem installing Calibre updates and other new applications then it would appear there may a permissions problem to the folder mentioned or the account used. But, for myself, I would not worry about this unless you have an ongoing problem.

But for the sake of good housekeeping and good order, after the new 8.1 update did you reboot the PC before you installed the Calibre update (I know the update reboots the PC 1 or more times itself, but did you take it upon yourself to do another)?

Also, after installing new update to 8.1 did you do another manual check for updates? Depending on the version of 8.1 you will likely get another couple of updates to add to those just installed, their installation being dependant on the existence of the previous ones. I doubt any omission of these would have resulted in the message you got, but mention it just from a housekeeping point of view.