That screenshot you posted says:
- Erasing 1fc00 to 1FFFF
- Programming 7FEC
That has erased from 127k to 128k. So it is smart enough to have erased the entire FLASH, assuming it started from zero (or above any internal loader). It knows how big it is.
From the Reference Manual, the MCF51JM128 FLASH address range is from 0x00000000 to 0x0001FFFF, which matches that.
I'd suggest reading the S7 file. It is ASCII with addresses in the first column. Make sure it is compiled with the right address range to fit in the FLASH. Make sure you don't have a restricted compiler that will only generate 32k.
The other option is to make your code more efficient and smaller. I always find I have to do that eventually!
Tom