I don't have an answer, but I can provide some information that might be of use in finding the answer.
The relevant information is stored in the Arduino IDE's preferences file. You can find the location of that file by opening the Arduino IDE's File > Preferences and then checking the line following "** More preferences can be edited directly in the file"**.
Note that this preferences.txt file is only read when the IDE starts up, and only saved when the IDE is closed. Keep this in mind if you are reading or editing the file while the Arduino IDE is running.
My suggestion would be to open that preferences.txt file in a text editor to see whether the IDE wrote the relevant information to it correctly. It uses a key=value data format similar to an .ini file.