I'd guess the SD card is a newer/faster one and doesn't get reset properly after the initial boot and thus can't be read-from. If you find an old/slow SD card without fancy fast modes it will probably work. Using the USB adaptor sidesteps such issues.
NB: AMLGX is not perfect. If you want to nit-pick on what works/doesn't, you can save fingers from typing forum reports about this/that test file because a) I know there are bugs, b) I know nobody is working to fix them. I'd like to see improvements of course, but until there are some, the reports aren't interesting. Best results come with using the mode whitelist and adjust-refresh. Using "sync playback to display" will probably cause more issues that it might solve. If it works for you, that's nice. If it doesn't,