Looks like what muddafudda says is spot-on, it could indeed be the checkpoints.
static MapCheckpoints mapCheckpoints =
boost::assign::map_list_of
( 1500, uint256("0x841a2965955dd288cfa707a755d05a54e45f8bd476835ec9af4402a2b59a2967"))
;
You've got Litecoin's block 1500 hash as your first checkpoint. You need to remove the 841a2965955dd288cfa707a755d05a54e45f8bd476835ec9af4402a2b59a2967 after
uint256("0x then put your genesis own block hash in instead and recompile.