That is interesting. I HAVE seen something like this..where the MIST seems to drop key events in some circumstances. I mostly ran into it when doing high speed bursts of input at the interface, first with a keyboard emulating barcode reader, then later when trying to send input to the MIST with an Arduino Micro as an HID device. It would seemingly randomly drop keydown and keyup events. When it would drop keyups, the keypress would repeat forever unless I sent more keyboard input to the interface.
Ironically, I NEVER saw this in the ST core, but I did see it in all of the others I tried, especially in the Amiga cores. The ST core has always been rock solid for me and seems to handle whatever I throw at it.