Nemurenai,
There's a fairly simple demonstration of your point that can be taken from the Win32::API docs - one that doesn't need a laptop to test out.
Save the following file as 'mymod.pm':

package mymod;
use warnings;
use Win32::API;

#### define the structure
Win32::API::Struct->typedef( POINT => qw{
    LONG x;
    LONG y;
});

#### import an API that uses this structure
Win32::API->Import('user32', 'BOOL GetCursorPos(LPPOINT lpPoint)');

#### create a 'POINT' object
my $pt = Win32::API::Struct->new('POINT');

#### call the function passing our structure object
GetCursorPos($pt);

#### and now, access its members
print "The cursor is at: $pt->{x}, $pt->{y}\n";

1;
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When you run that file as 'perl mymod.pm' you get output like the following (depending upon just where the cursor is located):

D:\pscrpt>perl mymod.pm
The cursor is at: 584, 1017

D:\pscrpt>perl mymod.pm
The cursor is at: 213, 542
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Next, try running the following script (named 'test.pl'):

use warnings;
use mymod;
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That consistently produces the following output for me (with an accompanying segfault):

D:\pscrpt>perl test.pl
Win32::API::parse_prototype: WARNING unknown output parameter type 'BO
+OL' at D:/
perl58_M/site/5.8.8/lib/Win32/API.pm line 273.
Use of uninitialized value in concatenation (.) or string at mymod.pm 
+line 21.
Use of uninitialized value in concatenation (.) or string at mymod.pm 
+line 21.
The cursor is at: ,
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I can't offer a useful explanation of this ... but I guess it has something to do with the quirky way that Win32::API::Struct goes about doing whatever it is that Win32::API::Struct does.

I don't think that Win32::API::Struct enables you to do anything that can't be done by using simply Win32::API.
Win32::API::Struct merely simplifies the coding that's necessary. So you should be able to rewrite your code (using only Win32::API) in such a way that avoids the odd behaviour you've noted.

Cheers,
Rob