Wow, thanks for the quick response.
I checked the .cue file and every .bin is listed there (only for disc 1, since I am in disc 1 folder. There is a separate .cue file for disc 2 folder)
If I understood correctly, should I separate the .bin files from the .cue file and have two folders, one for .bin and one for .cue?
Right now it is structured like this:
Main folder (Disc 1)->.bin files and corresponding .cue file
Main folder (Disc 2)->.bin files and corresponing .cue file
From Launchbox frontend (after importing the folders, disc1 & disc2) , the file that is run is the track01 .bin file from disc 1