After boiling down the needle-in-haystack problem and dropping all but the necessary lines, I have the following three files:

File Baseclass.pm

package Baseclass;
use strict;
use subclass1;

print "load Baseclass\n";

sub new  { 
    my $class = shift;
    return bless {},$class;
}
1;
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File Subclass1.pm

package Subclass1;

use strict;
use warnings;

use base( "Baseclass" );

sub new {
    my $class = shift;
    return $self  = $class->SUPER::new(@_);
}
print "load Subclass1\n";
1;
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File Bla.pl

use strict;
use warnings;
use Subclass1;

my $obj = Subclass1->new;
1;
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Now run perl bla.pl and you get the following output:

Load Subclass1
load Baseclass
Subroutine new redefined at Subclass1.pm line 11.
Load Subclass1
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Now, here comes the solution.

It is simple but not really obvious in the sense of visible. It is the letter 's' or should I say 'S'?
In file Baseclass.pm line 3 uses 'subclass1' instead of 'Subclass1' with capital letter. Perl sees two modules use Subclass1; and use subclass1;. Windows does not care about case and gives Perl the file Subclass1.pm both times.

Hope this helps somebody, save your day for better things.