Did you do as I suggested and examine the list of transactions? You say, “The problem seems to affect almost all the transactions.” What does that mean? Which ones? What type of transactions in which tabs? New transactions? Previous transactions?
Whether you have one transaction or hundreds, Manager will behave the same way when generating automatic reference numbers. It finds the highest existing number and adds 1. But the program does not change previous transactions. If those had no reference numbers, they won’t after updating the software. If any of them did, the reference numbers they previously had will be kept, and new transactions will pick up from the highest one.