I found three transactions for some reason were marked with a “C” in the register that tallied to $1,877.50. I reconciled in register and marked them with an “R"
It then said the beginning balance is off, as they were from a previous reconciliation. I then realised they were in fact duplicates.
What was confusing was that I was selecting the period 30/12/20 to 30/3/20 and these 3 payments were showing in the tally of the total payments. It would have been nice if it was highlighted that the three hidden transactions were from the previous period.
I have also realised why I was getting duplicates in the first place. I had been using a third party plugin to scan receipts and these weren't always matching what was in the banking tab. Maybe safer to add and match transactions in the banking tab in future.