I created a symbol LM324.qsym, where the .SUBCKT defines the ports as 1 2 99 50 28. I then deleted the file LM324.qsym as I had messed-up something. Now when I try to create a fresh version of the symbol by pasting in the .SUBCKT the auto-generate function in QSPICE allocates port numbers exactly 1 greater i.e. 2 3 100 51 29. Closing QSPICE and restarting Windows has no effect. I have not checked to see if the symbol works in a simulation as I was more concerned about the port numbers being wrong.
This problem has disappeared since QSPICE updated, I’m not sure if a specific update fixed it, or just the act of any update.
Good news. Thanks Steven.