It's easy to manufacture example code that shows something like the behavior you report:

c:\@Work\Perl\monks>perl -wMstrict -le
"my $x;
 ;;
 S('A');
 ;;
 $x = 'foo';
 ;;
 S('B');
 ;;
 sub S { print qq{$_[0]: x is }, defined $x ? qq{'$x'} : 'undefined'; 
+}
"
A: x is undefined
B: x is 'foo'
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This simple example code always produces the output shown. It's easy to imagine that in your "much more complex" code different execution paths are sometimes taken, such that your equivalent of  $x has, on occasion, already been initialized when subroutine  S() is called at point 'A'. In any event, I hope it is clear why  $x is uninitialized at point 'A' and initialized at point 'B'.

Update: See also the discussion in response to subroutine no error.