What I often do is to apply settings, hit exit and reopen (settings is saved and still there) the app before i run the process. This specially applies to RTKconv and sometimes in RTKpost.
I created multiple instances of the rtk executables for the purpose of saving different settings… but I did find that I had to close it and reopen it every single time to run it or there were errors.
I have seen it with many different datasets, and after deleting the .ini and starting fresh, the problem usually goes away.
Maybe the ini file (when it happens) is of more value to you ?