Is it possible you stopped at Confirm Matches and didn't finish the reconciliation? If you stop there, when you next go into Bank Feeds you must choose to "Use saved", otherwise it starts again from scratch. The box on the right, annoyingly, defaults to just the most recent transactions so make sure you check the box at the top right to make sure nothing is excluded.  

If none of these things are the problem and you have previously reconciled the transactions, it's possible that the bank feed has been duplicated.  There were issues with some high street banks over the Christmas break, sending duplicated data.  If so, you can just select and Ignore those duplications. This Sage video may help https://www.youtube.com/watch?v=gX6ip8BF1l4

Thanks for your response, I'm unable to find the Use Saved option for some reason unless that shows up during reconciliation. And there's no duplicates, thankfully! Although I have experienced those in the past.

I've just went back in and tried to match one transaction to test, and same thing is happening after I press Confirm Matches. It takes me back to the Bank Accounts window as if it has been successful. 

So I managed to resolve it. I had to raise a case on sage.com and was then advised to phone technical support so they could remotely access my computer to delete some background files.