System Disk (this data that land on the A: drive) are divided into (if I remember right ) 32K blocks - first block which contains Menu bitmap and links to the installed program is not checked in any way, but the other segments are. I have seen using mem (MSDOS standard program), maxmem (made by me) that Memdisk.sys handles drives from B: to V: (i used "mem/d" command to see it). I have spent a lot of time to make up 16/32 bit CRC for the whole system disk or it's 32Kb blocks - with same result - Memory reset.

I also think that making "fixed" boot sequence by comparing ROM with Flash contents is quite stupid, but than again Casio engineers... ;-)
It would be really nice to take over the boot sequence, get rid of Launcher,Launchtsr, and install your own file explorer. The other soultion would be overwrite the system memory with system image that hasn't got those files installed, but this is dirty solution.
Roeoender.