Yes, i am sure, i test it on XDT512 and XEP100.
Using PROG12Z with pemicro&multilink you have to select one algorithm.
For xdt512 it had two algorithms:
9S12XDT512_1x16x2k_4k_EEPROM_linear_1k_page
9S12XDT512_1x16x256k_512k_Linear_16k_page
in xep100 it have three algorithms:
9S12XEP100_1x16x512k_1024k_Linear_Pflash
9S12XEP100_1x16xmax2k_max4K_EEPROM_linear_1k_page
9S12XEP100_1x16xmax16k_max32k_Linear_User_Dflash
In summary, if you have a .s19 or .elf or .abs file with linear addresses, you must be select the appropriate algorithm to program the flash.
For example, is you srecord file have data on EEPROM and IFLASH, you must be select first the eeprom algorithm, program the device, and then select the other algorithm and program the flash.
With USBDM you only can program the IFLASH.
With NoICE12 you have the same problem, independently, if you use pemicro multilink or USBDM.