By racking the beer, you're taking the beer off the yeast cake. I'd also assume it's in secondary longer; therefore, less yeast in suspension. Less yeast in suspension would mean slower carbonation. I've bottled some very clear lagers without additional yeast and they've carbonated fine, but slowly. The only time I've added yeast is a Pre-Prohibition Lager that I clarified with isinglass. To know for sure, you should split a batch - rack half of the beer and leave the other half alone. Bottle both at the same time and see if there's a difference in time to carbonate. But in reality, as long as the beer is carbonating, don't worry about it.