Well, if "MKS" is an alternate shell, and it runs when you type "cmd.exe", there is nothing perl related you can do to fix the problem

cmd.exe should always start cmd.exe, if it doesn't, uninstall whatever is posing as cmd.exe

OTOH, you might be able to (but it probably won't work), to recompile perl under MKS... there is such a thing as "mksperl"