As it was explained to me in a while ago when I was having a similar problem/question with a similar problem that  you are experiencing ---  this may have provide some basic explanation on what you were experiencing. If I am wrong, I am sure someone will correct me.

AC Log is not a contest logging program. It is just a general log

Per an agreement between Dave and Scott, Both do not support every contest. By that I mean, N3FJP has specific contest loggers that are supported by FLDIGI, but not all are such as the BARTG RTTY. N3FJP has no contest log for the BARTG contest. Thus if you try to use the AC Log with the API in AC Log Enabled and the connect box checked in FLDIGI under N3FJP Logs , then it causes FLDIGI to act in a way that you do not want it to for the contest and it reverts back to the  general N3FJP Amateur Contact Log setup. That is why when you closed AC log, FLDIGI started to log the serial numbers as you wanted it to. You probably selected in FLDIGI under contests the BARTG RTTY contest and when it did not find any N3FJP Program, it did not change and worked as you expected it to.  You can see with N3FJP program is being queried and used at the top of the FLDIGI screen.

If you use the proper N3FJP Contest logging program, and have both API in N3FJP Contest Logger and The box in FLDIGI LOGS checked, the FLDIG will automatically pick the proper contest and load the proper default fields and both will work together properly. This however, is expecting  you to have your macros properly written and used in FLDIGI.

When you have the API enabled in AC Log and AC Log selected in FLDIGI, FLDIGI will revert from any contest  you select to the generic FLDIGI setup, thus eliminating the serial number function.

Hope this helps some

Larry  N8CWU