What I can work out is that the MAKERbuino software is based on or the same as used by GAMEbuino.
I can only predict that this sounds like a reading issue from the SD card which has corrupted the processor memory, this then causes the current issue you are experiencing. Pin pointing the software issue isn't going to be an easy task.
The MAKERbuino SD card has a file called LOADER.HEX, See GAMEbuino wiki which explains the following:
If the C button is held down while the unit is powered-up then the bootloader will search for a compiled sketch on the SD card called "LOADER.HEX".
This will then reset the bootloader and in turn fix the issue.
The GAMEbuino wiki link HERE