The windows version of Popstation is geared towards files made by CloneCD. It doesn't understand the format of toc/cue files made by other programs, so you lose the CDDA. I made a python script for linux to make my own EBOOTs - theoretically, it should also work with OSX, but it didn't due to the crazy way OSX forces you to access the CD. I still need to work on that more.
At the moment, the only way I know you could get this working on a Mac is to run Windows in an emu and run the Windows apps... or install linux on the Mac and use my python script.
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