I haven't done much with Win32 in perl and others have already stated the whole 'can you get the build version' but from what was given, it seems we know the following:

1. build versions are the only difference in the given chart
   
2. .NET has 36## for build version
   
3. 2003 has 37## for build version
   

First, since I don't know what the variables are for Config, I do the following:

foreach $i (keys %Config) {
  print "$i\n";
}
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Perhaps a set variable based on what the build version is?
Example:

$build_prefix = substr Win32::GetBuild, 0, 2;

if ($build_prefix == '36') {
  # do something for .NET
} elsif ($build_prefix == '37') {
  # do something for 2003
}
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Course, it'd be better if I knew for sure you could get the build version from Config or Win32, but it's a helping hand! I'm probably going to go look it up soon anyways just to know, hehe...

EDIT: after looking back over this, it seems the above code/etc is a really kludgy way of doing it and I probably should've done my homework before posting. Bah, I say...it's 12:30 and I'm still at work!