Thanks for both answeres, yes the problem is vague, and vague to describe...
We have as string and have the internal utf8 flag switched to on:

# my example may be any string from a database /user input etc.
my $example = "just a string that i nééd to be utf8 encoded, but can't
+ see it in the chars, so guess::encode won't work";
Encode::_utf8_on($example);

# ...
use open ':utf8';
use open ':std';
#...
my $cgi = new CGI;
print $cgi->header(
    -type        => 'text/html',
    -expires    => '-1d',
    -cookie        => [$cookie],
    -charset    => 'UTF-8',
)
print $example;
[download]

Now the first time it's called using mod::perl regestry it prints:

just a string that i nééd to be utf8 encoded, but can't see it in the 
+chars, so guess::encode won't work
[download]

but the second time:

just a string that i nééd to be utf8 encoded, but can't see it in th
+e chars, so guess::encode won't work
[download]

This is weird, and i have no controll over how mod perl internally stores it's values.

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