Two issues. Well, one GUI behavior question that might turn into an issue, and then a configuration setting issue. The first is fairly cut and dry, but the second is a bit lengthy due to describing the scenario and then some conceptual discussion.
1) When you hit the X to "close" the GUI, if you're using the DSP version, you're not really "closing" the application. All you're doing is minimizing to tray, however the DSP version writes settings data to disk when being trayed. It does not write when it is just minimized. In my opinion, it doesn't need to write the data when being sent to tray, and the behavior of minimize and tray should be the same.
2) While I was trying to go to sleep last night, I got to thinking about the Quality slider. Yeah, it is that hard for me to go to sleep.

Anyway, I understand the reasoning behind not wanting to lower the quality if it doesn't need to be lowered, but how about if viewed from the opposite perspective, i.e. someone with a less-capable machine? What can then happen is the user, a potential paying customer, is presented with the default configuration being "maximum quality". If they don't have the hardware for maximum quality and that's what they're given as the default, in my opinion, that doesn't make a good first impression. Yes, you can indeed change that configuration, but the first impression was already made.
Because my development experience was for a Fortune 500 company and a government entity, the idea of "self-healing" and "user-friendly" software got hammered into me. Self-healing is still a stretch as it borders on Artificial Intelligence. That's not efficiently doable at this point, but software that has performance metrics built into it and can be adaptive based on how efficiently a test data set is processed is certainly doable.
Case-in-point: Winamp's "Modern Skins"
Modern Skins have a "Timers Resolution" setting on the General tab for that component's preferences. What this maps to in Stereo Tool is the "Display Refresh Speed" setting just below the Quality setting. In Winamp, there is a button that you can click that says "As fast as possible for this machine". You play some audio, and it runs a test to select what it feels is the fastest recommended setting.
I think it would be good for Stereo Tool to have something similar. It could be run manually at any time, but it would automatically run a test at installation and would provide the user with some sort of notification of what it has determined to be the "recommended setting". I would think it should also run any time the number of samples are changed. What would really be cool is if there was a separate quality setting for each number of samples setting (512, 1024, 2048, 4096).