Note that it is NOT !!!! MISO/MOSI that you use to program a M128 , you use the same pins as for Uart1 i think ....
Do NOT connect the PEN pin to anything on the M128.
If those things are observed then you can program a M128 the same way as the other Mega's.
Btw: As the M128 comes with the 1Mhz internal clock enabled , you might want to check that your programming clcck is not set to high (ISP Clock) (with respect to the 1 Mhz it is using at the first programming cycle)