Good question, but since the MKV is working now I assumed the new question would only complicate things. Maybe the two aren't related. But no problem if the topic is merged with the other thread.
Are you always running the pineapple with an SD card inserted? Yes
A. Use the Format SD card function then reboot Yes and then
B. (while an SD card was inserted) try a reflash of the firmware from the web interface? Yes
And it didn't solve the problem.