Ok i *think* i can take a guess about this..
The way BrowserTraySwitch (now) works, is that is saves snapshots of the current DEFAULT settings.
When you use a commandline parameter to launch firefox with a certain profile, it's actually telling firefox NOT to change the default setting, and only to run one time with your specified profile. So when you tell BrowserTraySwitch to memorize the current default settings, there is nothing for it to record.
So i think the first step would be to try CHANGING THE DEFAULT PROFILE in firefox to each of your different profiles in turn, and asking BrowserTraySwitch to save each time you do as a new configuration.
Now if that does not work, which it may not, it just probably means that BrowserTraySwitch is not memorizing the registry value that stores the value saying what profile is set in FireFox (assuming that it is a registry settings). If that's the case, contact me and i'll see if i can add it (and if you can find the registry setting that records what profile is set as default that would help).