One day everything loads up fine, the next day some bonkers error box pops up with no files having been moved, changed adjusted or in any way mucked about with.

"Master file hiboriamain.esm does not match the one on the network."

I then get the rare opportunity to copy the file via the CS. Having made a backup of the file before attempting to follow any CS advice, I am wondering exactly what the CS is suddenly banging on about.

Any ideas?

Sounds like nothing to do with CS, and more to do with Windows. Are you using Vista or Win 7, and do you have UAC active? Is the game installed into the default directory or into a custom location like C:\Games\Bethesda Studios\Oblivion\