It's related to the address-pubkeyhash-version value from your blockchain's params.dat file. However by default MultiChain uses 4-byte values for that, which will not be compatible with your vanity key generator.
So instead you should start a new chain, and set address-pubkeyhash-version to a 1-byte value (two hexadecimal digits) before you launch the chain. You should probably choose something other than 00 to make sure your addresses can't be confused with those of bitcoin. Note you'll also need to set address-checksum-value = 00000000 in params.dat as well - again, before starting the chain - so your vanity generator works.
