I think system() returns the exit status of the command ( i.e. $? ) -- so if your command executed properly, then it would most likely return a 0, which is a logical "false" for perl. So you need to warn when:

   system( "$your_command" );
   if( $? != 0 ) {
      warn "something's wrong";
   }

   ## or
   ##    ( system( "$cmd" ) == 0 ) or warn "the sky is falling!";
   ##
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I don't know about the illegal seek stuff, but I used to get a lot of that when I would have bogus errors ( i.e. my bug ) in the code. It's probably just that $! was never meant to be set when you checked for it ( however, I'm no expert on this subject, so please take that statement with a grain of salt )