But I installed it via ppm and NOT from cpan. But I think that this shouldn't make a difference
If you have the capacity (ie a auitable compiler) to build Win32::Exe from source, maybe do that and see if it makes a difference. (You're right, it shouldn't make a difference.)
Also check to see how Win32::Exe goes at creating the icon for an exe file that has *not* been created by 'pp'.