Adjusting recipes for counterflow chiller?

After increasing batch sizes from 5 to 10 gallons, I elected to upgrade from an immersion chiller to a counterflow chiller.  It is a very effective chiller for the price.  I have made a number of good batches with the new equipment and for the most part I have been pleased.  My only issues involve the hops.  The beers, especially PAs and IPAs, have a lingering bitterness and fall short in the aroma department even with heavy hop additions at flameout.  After reading a couple BeerSmith blogs on late hop additions, in particular http://beersmith.com/blog/2013/01/21/late-hop-additions-and-hop-oils-in-beer-brewing/, it got me wondering.  If it typically takes 25 minutes to run the worth through the counterflow chiller, am I loosing some of the essential oils?  Additionally, if the wort remains above 200 degrees for 25 minutes, does that impact the the overall IBUs of the recipe?  It seems to me that I may be squeezing more out of my mid and late addition hops than the design accounts for.  Not sure if anyone else has encountered this problem or can offer any advice.  My initial "fix" is to create a cooling whirlpool through the counterflow chiller for 15 minutes allowing the wort to drop to 150, then transferring through counterflow into the fermenter.  Even then I am not sure if my recipes need to be adjusted.  Thoughts?  Advice?