For those of you who are interested here is what I have found.
After finally getting the machine sent to me I have been able to run some tests on it. I think I mentioned earlier I got a tech to have a look at it. He did a number of test with chkdsk being one of them but didn't find any issue.
Once I got it and ran a chkdsk I got a number of errors which have now been corrected. Since then when running things like diskclean I don't get the 'unknown publisher' error. I can also install updates.

Thanks to all of you for your advice and assistance.