MultiDisk No longer works

[cwmd]

I have a pi3 and it is running retropie 4.2 loaded with ApplePi-Baker, While on version 3.6 or so I was about to go to quick menu and append the image of whatever disk was next but after updating to 4.2 when I try to do this the folder appears empty. All the roms are .bin but I have tried .iso and eboot. When launching a game or browsing the file system you can see all the files but when attempting to do the disk swap the folder will appear emtpy. I tried starting fresh with a format of the sd card and loaded the image completely new and the issue is the same. I have searched these forums and I have spent several hours online trying to figure this out but I can't seem to find anything like this issue. I have also read through all of the config files for retroarch looking for something that might be hiding certain file ext. I am still very new to the raspberry pi and any help would be appreciated.