I think the problem is that you are passing a ref to 0x03 when you want to pass the value itself. I have no idea if your conversion leads to &PCICARD_SET_REGISTER returning a value. This is simply an integer, so given you can check the value in your working C code, and check what you have in your Perl would be a good sanity check. Obviously these values need to be the same. Also you don't check your file open worked although I don't see why it should fail given you have sufficient permissions to do the open in your C. I would suggest:

#!/usr/bin/perl

require 'sys/ioctl.ph';
require '_h2ph_pre.ph';

sub PCICARD_IOC_NUM () { ord('0'); }
sub PCICARD_SET_REGISTER () { &_IOR( &PCICARD_IOC_NUM, 1, 'int' ); }
sub PCICARD_GET_REGISTER () { &_IOW( &PCICARD_IOC_NUM, 2, 'int' ); }

# Sanity check.....
print "PCICARD_SET_REGISTER is %d\n", &PCICARD_SET_REGISTER;

# you may need $value = pack 'C', 0x03
# as this will pack 0x03 into an unsigned 8 bit (char) value 
$value = 0x03;  

open(PCI, '+</dev/pcimax') or die "Can't open card $!\n";
ioctl(PCI, &PCICARD_SET_REGISTER, $value) or die "ioctl error $!\n";
close(PCI);
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As a last resort you could just dump your working C code into an Inline::C function. Sometimes this is the easiest thing to do.