When running updates for GSX I get this message
Why you think it's an "error" ? Do you see any error warning sign or indication anywhere ? It's just a progress bar label that says: since you don't have that specific product installer, the Live Update won't update its related file for it.
.Now as far as I am aware GSX is running fine after the update but should this happen?
Yes, of course it should happen. The issue is, since that's NOT an error, and it's a running progress bar message, if it displayed a message like:
"I'm now trying to update XPOI, but since you don't seems to have XPOI installed, I'll will skip the xxxxxxx.yyy file name which is supposed to be installed in case you had XPOI installed, so I'll skip it and go to the next one"
There would no time to read it, because it's a progress bar. If it WAS an error, we wouldn't use a progress bar, but a warning MessageBox that would STOP you, indicating some kind of problem.
And, it seems you have an outdated version of the updater program ( the current one can be obtained by downloading the current Stand-Alone Addon Manager or any other product full installer, like GSX for example ), because the latest version comes with a progress message which is a bit more clear:
"The product the file xxxxxx.yyyy belongs to is not installed, no need to download it"