First of all, use the CODE tags: 
package myPackage;
my @containerRefArray=();
my @containeeArray=(); 
 ... 
sub get_parentRelPos (\%$) { 
 my ($object, $name)=@_; 
 my ($i, $j, $found); 
 my @tmp; 
 my $parentObject=$object->{'~PARENT'}; 
 my $objectIndex=$object->{'~entPhysicalIndex'}; 

 for ($i=0; $i < @containerRefArray; $i++) { 
  if ($containerRefArray[$i] eq $parentObject) { 
   $found=1; 
   last; 
  } 
 }
 ...

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Second - based on the code you've given with no other info, it's obvious why your array is empty. I can only assume that somewhere in the snipped portion of your code do you actually do something with @containeeArray, because I don't see it used at all in the code example. Are you using it as a parameter to get_parentRelPos?
We need more info before we can help!

Update: Hmmm...Apparently somebody edited the top level node and added CODE tags...

Guildenstern
Negaterd character class uber alles!

In reply to (Guildenstern) RE: Array mysteriously disappears on loop exit... by Guildenstern
in thread Array mysteriously disappears on loop exit... by Anonymous Monk

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