there will be a space between the hot end and the bed if you are running G29 stand alone. Try doing a calibration cube or something small with G29 added to the custom G-code after the G28 and see if it prints properly.

That's odd that your having trouble with it flashing the memory, Just to cover all of your bases be sure to use the short USB cable provided by Colin, because interefence can be had with longer cables, If that doesnt help there is a chance that there could be an issue with the flash. If that's the case contacting Colin for a replacement board will be your only option just test extensively