Thanks for the response, Tursi.
I ran the debugger but didn't find anything. No messages outside the normal operating messages. During the process, I was exploring the Infocom disks as well as some others. It seems that classic99 can't actually read the disks. Either the V9T9 format or the FIAD format (the DSK1 contents that are default with classic 99, too) when I go to a disk manager and try to get a catalog it gives a partial disk name and and empty disk. All of the Infocom disks I checked give a no disk found error (7, I think). These exact same disk files work fine on the WinXP VM. It would appear that there's a file system read problem., but I'm not sure how to approach it.
I checked the same disks under MESS and they read fine. Here I get the green screen and freeze up when trying to start Leather Goddesses of Phobos while other Infocom disks work (Planetfall, Zork, Ballyhoo).