Urm, I don't want to set a cat amongst the pigeons here, but after performing a factory reset (it is so much easier to restore everything after a FDR nowadays than it was a few years ago!), things are a LOT smoother!
Here's why I think they are:
Samsung stated in their reply above, and subsequently their reply to me (word for word as above), that "old systems settings can be left on the phone" and I think I know what they mean; can anyone find "Developer Options" on their 4.3 afflicted GS3? I can't, but I they were available on 4.1.2 because I had all the window animations etc switched off.
After updating to 4.3 initially, my brain noticed no difference at all to the window animations / slide into view stuff which means that they must still have still been switched off, because the second I performed the FDR and went into my apps, my brain noticed that they were back! I tried to find the developer options, but couldn't.
So, is it possible that these options, along with other changed or removed options, resident from the previous firmware have messed up other people's phones? Are Samsung actually talking sense...?
After my FDR and seeing the difference compared to pre-FDR, I'd strongly recommend anyone to do the same. Just don't expect to be able to switch the annoying window animations off (gonna take me a while to tolerate them!).